Tools

Suite ID	Suite version	Tool IDs	Description	EDAM topic(s)	EDAM operation(s)	Suite runs on main servers	bio.tools (if available)	Conda id	biii	Status	Availability across Galaxies
source_extractor_astro_tool	0.0.1+galaxy0	source_extractor_astro_tool	Tool to extract luminous sources from astronomical sky images			0		astropy		To update	UseGalaxy.eu1
sgwb_astro_tool	0.0.1+galaxy0	sgwb_astro_tool	SGWB			7		ipython		To update	UseGalaxy.eu1
plot_tools_astro_tool	0.0.1+galaxy0	plot_tools_astro_tool	Plot Tools			0		pandas		To update	UseGalaxy.eu1
hess_astro_tool	0.0.2+galaxy0	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope			2		ipython		To update	UseGalaxy.eu1
grb_detection_astro_tool	0.0.1+galaxy0	grb_detection_astro_tool	SPI-ACS GRB detection			0		numpy		To update	UseGalaxy.eu1
fits2tiff_astro_tool	0.0.1+galaxy0	fits2tiff_astro_tool	Tool to convert FITS files to TIFF			0		astropy		To update	UseGalaxy.eu1
desi_legacy_survey_astro_tool	0.0.2+galaxy0	desi_legacy_survey_astro_tool	Tool to query Legacy Survey data			0		astropy		To update	UseGalaxy.eu1
cta_astro_tool	0.0.1+galaxy0	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package			1		unzip		To update	UseGalaxy.eu1
crbeam_astro_tool	0.0.2+galaxy0	crbeam_astro_tool	CRbeam			0		crbeam		To update	UseGalaxy.eu1
astropytools	0.1.0+galaxy1	astropy_csv2fits astropy_fits2bitmap astropy_fits2csv astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations			13		astropy		To update	UseGalaxy.cz3 UseGalaxy.eu4
astronomicalarchivestool	0.10.21	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy			55		astropy		To update	UseGalaxy.cz1 UseGalaxy.eu1
analyse_short_astro_text_astro_tool	0.0.1+galaxy0	analyse_short_astro_text_astro_tool	Tool to analyse short astrophysics texts			0		astroquery		To update	UseGalaxy.eu1
xlsx2tsv	0.1.0+galaxy0	xlsx2tsv	Convert an xlsx file to a tabular			0		pandas		To update	UseGalaxy.eu1
virsorter	2.2.4	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	Metagenomics	Taxonomic classification	344	virsorter	virsorter		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
vibrant	1.2.1	vibrant	Virus Identification By iteRative ANnoTation	Metagenomics Microbial ecology Sequence assembly Molecular interactions, pathways and networks Endocrinology and metabolism	Sequence trimming Scaffolding Genome annotation	19	VIBRANT	vibrant		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
dose_response_analysis_tool	3.0.1	dr_curve	A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses			0		r-drc		To update
baseline_toxicity_calculator	0.1.0+galaxy0	tt_baseline	Toxicity prediction using QSAR models			0		pandas		To update
scripting tools	0.3	singularity_scriptrunner	suite_scripting			0				To update
saqc	2.6.0	saqc saqc_executor	System for automated Quality Control			0		saqc		To update	UseGalaxy.eu1
phi_toolkit_report	0.2.0	phi_toolkit_report	Phage host interaction toolkit report generator			0		bioconductor-biostrings		To update	UseGalaxy.or1
phabox	2.1.11	phabox_cherry phabox_contamination phabox_end_to_end phabox_phagcn phabox_phamer phabox_phatyp phabox_phavip phabox_tree phabox_votu	Identify and analyze phage contigs in metagenomic data	Metagenomics Microbial ecology Sequence assembly Taxonomy	Sequence assembly Taxonomic classification Visualisation	0	phabox	phabox		To update
omero_upload	5.18.0	omero_dataset_to_plate omero_filter omero_get_id omero_get_value omero_import omero_metadata_import omero_roi_import	Interact with an OMERO.server using omero-py and ezomero.	Imaging Data visualisation	Image analysis	0	omero			To update	UseGalaxy.eu3
suite_ogs_tools	0.4.0	msh2vtu shp2msh	A suite of tools for OpenGeoSys (ogs)			0		ogstools		To update
suite_ogs	6.5.3	ogs_addlayer ogs_extractboundary ogs_extractsurface ogs_generatestructuredmesh ogs_identifysubdomains ogs_simulation	A suite of tools for OpenGeoSys (ogs)			0				To update
longorf	0.3.0	longORF	obtain longest ORF in six-frame translations			0				To update
lambdaminer	0.1.0+galaxy0	lm_get_projects	Lambda-Miner Tools			0		pandas		To update
iphop	1.3.3	iphop_predict	Integrated Phage Host Prediction		Sample comparison	0	iphop	iphop		To update	UseGalaxy.eu1 UseGalaxy.or1
genomad	1.11.1	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	Sequence analysis	Sequence annotation Taxonomic classification	1658	genomad	genomad		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
eukcc	2.1.3	eukcc_single	Galaxy wrapper for EukCC	Metagenomics	Sequence assembly validation	0	eukcc	eukcc		Up-to-date
dfpl	2.1	dfpl_predict dfpl_train	Galaxy wrapper for deepFPlearn.			0		deepfplearn		Up-to-date
dfast	1.3.6	dfast	Prokaryotic genome annotation	Nucleic acid structure analysis Genomics Sequence analysis	Genome annotation	0	dfast	dfast		Up-to-date
checkv	1.0.3	checkv_end_to_end	Assess quality of single-contig viral genomes	Metagenomics Sequence assembly Metagenomic sequencing Mapping	Sequence assembly Validation Read mapping	38	checkv	checkv		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
frogs	4.2.0	FROGS_affiliation_filters FROGS_affiliation_postprocess FROGS_affiliation_stats FROGS_biom_to_stdBiom FROGS_biom_to_tsv FROGS_cluster_filters FROGS_cluster_stats FROGS_clustering FROGS_demultiplex FROGSSTAT_DESeq2_Preprocess FROGSSTAT_DESeq2_Visualisation FROGSFUNC_step2_functions FROGSFUNC_step3_pathways FROGSFUNC_step1_placeseqs FROGS_itsx FROGS_normalisation FROGSSTAT_Phyloseq_Alpha_Diversity FROGSSTAT_Phyloseq_Beta_Diversity FROGSSTAT_Phyloseq_Sample_Clustering FROGSSTAT_Phyloseq_Composition_Visualisation FROGSSTAT_Phyloseq_Import_Data FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance FROGSSTAT_Phyloseq_Structure_Visualisation FROGS_preprocess FROGS_remove_chimera FROGS_taxonomic_affiliation FROGS_Tree FROGS_tsv_to_biom	Suite for metabarcoding analysis			60685		frogs		To update	UseGalaxy.fr28
ncbi_blast_plus	2.16.0	blastxml_to_tabular get_species_taxids ncbi_blastdbcmd_info ncbi_blastdbcmd_wrapper ncbi_blastn_wrapper ncbi_blastp_wrapper ncbi_blastx_wrapper ncbi_convert2blastmask_wrapper ncbi_deltablast_wrapper ncbi_dustmasker_wrapper ncbi_makeblastdb ncbi_makeprofiledb ncbi_psiblast_wrapper ncbi_rpsblast_wrapper ncbi_rpstblastn_wrapper ncbi_segmasker_wrapper ncbi_tblastn_wrapper ncbi_tblastx_wrapper	NCBI BLAST+			1560984		blast		To update	UseGalaxy.be16 UseGalaxy.cz16 UseGalaxy.eu16 UseGalaxy.fr16 UseGalaxy.no15 UseGalaxy.or16
make_nr	0.0.3	make_nr	Make a FASTA file non-redundant	Molecular biology Sequence analysis	Sequence alignment Genome annotation	0	make_nr	biopython		To update
blastxml_to_top_descr	0.1.2	blastxml_to_top_descr	Make table of top BLAST match descriptions	Sequence analysis	Sequence alignment Sequence annotation	265716	blastxml_to_top_descr	python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
blast_rbh	0.3.0	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files	Nucleic acid sites, features and motifs	Gene functional annotation Nucleic acid sequence analysis	27781	blast_rbh	biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
blast2go	0.0.11	blast2go	Maps BLAST results to GO annotation terms	Nucleic acid sites, features and motifs	Gene functional annotation	1248	Blast2GO	b2g4pipe		To update	UseGalaxy.cz1 UseGalaxy.no1
upload_roi_and_measures_to_omero	0.0.5	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server			0		omero-py		To update
revertr2orientationinbam	0.0.2	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.			578		samtools		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
omero_hyperstack_to_gastruloid_measurements	20240214	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements			0		fiji		To update
omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels			0		fiji		To update
omero_get_full_images	20240521	omero_get_full_images	Get full images from omero			0		fiji		To update
omero_get_children_ids	0.2.0	omero_get_children_ids	Get omero id of children of an omero object id			0		omero-py		To update
omero_clean_rois_tables	20230623	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down			0		fiji		To update
measure_gastruloids	20221216	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index			0		fiji		To update
max_projections_stack_and_upload_omero	20241213.2	max_projections_stack_and_upload_omero	Combine images from max projections to stack and upload to the omero server			0		Fiji		To update
incucyte_stack_and_upload_omero	20231221	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server			0		Fiji		To update
hyperstack_to_bleach_corrected_movie	20241220	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack			0		Fiji		To update
gettn5extendedcoverage	0.0.2	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension			0		pysam		To update
fromgtftobed12	0.11.1+galaxy1	fromgtfTobed12	Convert GTF files to BED12 format			0		gffutils		To update
from_hicup_to_juicebox	0.0.2	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.			0		pysam		To update
cooler	0.9.3	cooler_balance cooler_cload_tabix cooler_csort_tabix cooler_makebins cooler_zoomify	cooler different tools to process Hi-C from mirnylab			534		htslib		To update	UseGalaxy.cz4 UseGalaxy.eu5 UseGalaxy.or4
suite_snvphyl_1_2_3			SNVPhyl suite defining all dependencies for SNVPhyl			0				To update
verify_map	1.8.2	verify_map	Checks the mapping quality of all BAM(s)			0		snvphyl-tools		Up-to-date
vcf2snvalignment	1.8.2	vcf2snvalignment	Generates multiple alignment of variant calls			0		snvphyl-tools		Up-to-date
snv_matrix	1.8.2	snvmatrix	Generate matrix of SNV distances			0		snvphyl-tools		Up-to-date
positions2snv_invariant_alignment	1.8.2	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.			0		snvphyl-tools		Up-to-date
positions2snv_alignment	1.8.2	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.			0		snvphyl-tools		Up-to-date
find_repeats	1.8.2	findrepeat	Find repetitive regions on a reference genome using MUMMer			0		snvphyl-tools		Up-to-date
filter_vcf	1.8.2	filtervcf	SNVPhyl filter_vcf			0		snvphyl-tools		Up-to-date
filter_stats	1.8.2	filterstat	SNVPhyl filter_stats			0		snvphyl-tools		Up-to-date
filter_density	1.8.2	filterdensity	Filter out position based on distance between SNVs			0		snvphyl-tools		Up-to-date
consolidate_vcfs	1.8.2	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment			0		snvphyl-tools		Up-to-date
xtb_molecular_optimization	6.6.1	xtb_molecular_optimization	Performs semiempirical molecular optimization.			262		xtb		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
wtv	0.1.0	wtv	A cli/python library for ion selection in mass spectrometry.	Metabolomics	Feature selection	0	wtv	wtv		Up-to-date
waveica	0.2.0	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	Metabolomics	Standardisation and normalisation	298	waveica	r-recetox-waveica		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
tables		table_pandas_arithmetics table_pandas_rename_column table_pandas_rename_columns_regex table_pandas_transform table_scipy_interpolate	Tools to manipulate and analyze data tables.			0		scipy		To update	UseGalaxy.eu5
spec2vec	0.8.0	spec2vec_similarity spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	Proteomics experiment Metabolomics Natural language processing Proteomics	Spectrum calculation Spectral library search Database search Natural product identification	115	spec2vec	spec2vec		Up-to-date	UseGalaxy.eu2 UseGalaxy.or2
rmassbank	3.0.0	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.			68		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
riassigner	0.4.1	riassigner riassigner_from_comment		Metabolomics Compound libraries and screening Data submission, annotation and curation	Standardisation and normalisation	302	riassigner	riassigner		To update	UseGalaxy.cz1 UseGalaxy.eu2 UseGalaxy.fr1 UseGalaxy.or2
retip	0.5.4	retip_apply retip_descriptors retip_filter_rt retip_train		Metabolomics Proteomics experiment Machine learning Cheminformatics Chemistry	Retention time prediction Spectrum calculation Deisotoping Formatting Deposition	0	retip			To update
rename_annotated_feature	1.0.0	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results			40		pandas		To update	UseGalaxy.eu1 UseGalaxy.or1
rem_complex	1.0.0	rem_complex	Removes molecular coordination complexes.			99		pandas		To update	UseGalaxy.eu1 UseGalaxy.or1
recetox-xmsannotator	0.10.0	recetox_xmsannotator_advanced			Expression profile pathway mapping Structure comparison Isotopic distributions calculation Annotation	133	recetox-xmsannotator	r-recetox-xmsannotator		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
recetox-msfinder	v3.5.2	recetox_msfinder		Metabolomics	Annotation	146	recetox-msfinder			To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
rcx_boxplot	3.5.1	rcx_boxplot	recetox-boxplot is a tool for plotting boxplots from a tabular/csv/parquet data file.			0		r-ggplot2		To update
recetox-aplcms	0.13.4	recetox_aplcms_align_features recetox_aplcms_compute_clusters recetox_aplcms_compute_template recetox_aplcms_correct_time recetox_aplcms_generate_feature_table recetox_aplcms_merge_known_table recetox_aplcms_recover_weaker_signals recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	Metabolomics	Chromatographic alignment Quantification Peak detection Feature extraction Alignment	2638	recetox-aplcms	r-recetox-aplcms		To update	UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr8 UseGalaxy.or8
rcx_tk	0.1.0	rcx-tk	Tools to process metadata or alkane files.			0		rcx-tk		Up-to-date	UseGalaxy.eu1
ramclustr	1.3.1	ramclustr ramclustr_define_experiment		Metabolomics	Imputation Standardisation and normalisation Clustering Correlation	859	ramclustr	r-ramclustr		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
query	0.2	query	Execute an SQL statement on a set of tables			0		click		To update
QCxMS	5.2.1	qcxms_getres qcxms_neutral_run qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).			36360				To update	UseGalaxy.eu3 UseGalaxy.or3
mztabm	1.0.6	mztabm_validate	Tools for handling mzTab-M files using various packages.	Ontology and terminology Metabolomics Data submission, annotation and curation	Loading Format validation Formatting	0	jmztab-m	jmztab-m		Up-to-date
mzspeclib	1.0.7	mzspeclib_convert mzspeclib_describe mzspeclib_validate	mzspeclib is a library and set of tools for handling, converting, and validating mass spectral libraries in a standardized format. This suite provides Galaxy wrappers for mzspeclib's core functionalities, including conversion and validation of spectral libraries.	Proteomics Metabolomics	Conversion Format validation	0	mzspeclib	mzspeclib		Up-to-date
mzml_validator	0.1.0+galaxy2	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.			0		lxml		To update
msp_merge	0.1.0	msp_merge				0		matchms		To update
msmetaenhancer	0.4.1	msmetaenhancer		Metabolomics Compound libraries and screening Data submission, annotation and curation	Annotation Standardisation and normalisation	287	msmetaenhancer	msmetaenhancer		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
ms2deepscore	2.0.0	ms2deepscore_config_generator ms2deepscore_similarity ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	Proteomics experiment Machine learning Metabolomics Small molecules Compound libraries and screening	Spectrum calculation Spectral library search Network analysis	0	ms2deepscore	ms2deepscore		To update	UseGalaxy.eu3
misc	1.0.0	target_screen use_theoretical_mz_annotations				186		pandas		To update	UseGalaxy.eu2 UseGalaxy.or1
MFAssignR	1.1.2	mfassignr_findRecalSeries mfassignr_histnoise mfassignr_isofiltr mfassignr_kmdnoise mfassignr_mfassign mfassignr_mfassignCHO mfassignr_recal mfassignr_recallist mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	Proteomics experiment Molecular interactions, pathways and networks Workflows	Visualisation	50	mfassignr	r-mfassignr		Up-to-date	UseGalaxy.eu9 UseGalaxy.or9
matchms	0.30.2	matchms_add_key matchms_convert matchms_matchms_export_skyline_transition_list matchms_filtering matchms_fingerprint_similarity matchms_formatter matchms_metadata_export matchms_metadata_match matchms_metadata_merge matchms_networking matchms_remove_key matchms_remove_spectra matchms_spectral_similarity matchms_split matchms_subsetting	Searching, filtering and converting mass spectral libraries.	Metabolomics	Spectral library search Format validation Filtering	4786	matchms	matchms		Up-to-date	UseGalaxy.cz9 UseGalaxy.eu14 UseGalaxy.fr11 UseGalaxy.or14
isolib	2.6+galaxy3	isolib	Create an isotopic pattern library for given compounds and adducts.			63		bioconductor-metabocoreutils		To update	UseGalaxy.eu1 UseGalaxy.or1
ipaPy2	1.3.0	ipapy2_MS1_annotation ipapy2_MS2_annotation ipapy2_clustering ipapy2_compute_all_adducts ipapy2_compute_bio ipapy2_gibbs_sampler ipapy2_gibbs_sampler_add ipapy2_map_isotope_patterns	Mass spectrometry data annotation tool.			0		ipapy2		Up-to-date
gc_derivatization	1.0.1	gc_derivatization	In silico derivatization for GC.			22		gc-meox-tms		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
freqsap	1.0.0+galaxy0	freqsap	Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP.			0		pandas		To update
filter_compounds	3.1.1	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.			0		openbabel		To update
biotransformer	3.0.20230403	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	Small molecules Endocrinology and metabolism Metabolomics Carbohydrates NMR	Metabolic pathway prediction PTM site prediction Natural product identification	67	biotransformer	biotransformer		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
bioconductor_scp	1.16.0	bioconductor_scp	scp is a package for the single cell proteomics data processing.	Proteomics experiment Proteomics	Visualisation Expression analysis	0	scp	bioconductor-scp		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
bioconductor_mzr	2.40.0	bioconductor_mzr_convert	Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows.	Proteomics Proteomics experiment Data management	Formatting	0	mzr	bioconductor-mzr		Up-to-date
bioconductor-msnbase	2.32.0	bioconductor_msnbase_centroid bioconductor_msnbase_smooth_chromatogram bioconductor_msnbase_smooth_mz	MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.	Proteomics Proteomics experiment Data management Data visualisation	Data handling Visualisation	0	msnbase	bioconductor-msnbase		Up-to-date	UseGalaxy.eu3
ucsc_cell_browser	1.0.0+galaxy1	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets			982		ucsc-cell-browser		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
suite_seurat	4.0.0	seurat_convert seurat_dim_plot seurat_export_cellbrowser seurat_filter_cells seurat_find_clusters seurat_find_markers seurat_find_neighbours seurat_find_variable_genes seurat_hover_locator seurat_integration seurat_map_query seurat_normalise_data seurat_plot seurat_read10x seurat_run_pca seurat_run_tsne seurat_run_umap seurat_scale_data seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1			5795		seurat-scripts		To update	UseGalaxy.eu14 UseGalaxy.fr11 UseGalaxy.or14
suite_scpred	1.0.2	scpred_get_feature_space scpred_get_std_output scpred_predict_labels scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0			25		scpred-cli		To update	UseGalaxy.eu4
suite_scmap	1.6.4	scmap_get_std_output scmap_index_cell scmap_index_cluster scmap_preprocess_sce scmap_scmap_cell scmap_scmap_cluster scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.			114		scmap-cli		To update	UseGalaxy.cz1 UseGalaxy.eu7
sceasy	0.0.5	sceasy_convert	Convert scRNA data object between popular formats			1998		r-sceasy		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
SCCAF	0.0.9	run_sccaf sccaf_asses sccaf_asses_merger sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.			111		sccaf		To update	UseGalaxy.eu4 UseGalaxy.or3
suite_scater	1.10.0	scater_calculate_cpm scater_calculate_qc_metrics scater_filter scater_is_outlier scater_normalize scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.			757		scater-scripts		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu6 UseGalaxy.no2 UseGalaxy.or2
scanpy_scripts	1.9.3	anndata_ops scanpy_filter_cells scanpy_filter_genes scanpy_find_cluster scanpy_find_markers scanpy_find_variable_genes scanpy_integrate_bbknn scanpy_integrate_combat scanpy_integrate_harmony scanpy_integrate_mnn scanpy_plot_scrublet scanpy_multiplet_scrublet scanpy_compute_graph scanpy_normalise_data scanpy_parameter_iterator scanpy_plot_embed scanpy_plot_trajectory scanpy_read_10x scanpy_regress_variable scanpy_run_diffmap scanpy_run_dpt scanpy_run_fdg scanpy_run_paga scanpy_run_pca scanpy_run_tsne scanpy_run_umap scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.			63989		scanpy-scripts		To update	UseGalaxy.be1 UseGalaxy.cz14 UseGalaxy.eu27 UseGalaxy.no13 UseGalaxy.or27
suite_sc3	1.8.0	sc3_calc_biology sc3_calc_consens sc3_calc_dists sc3_calc_transfs sc3_estimate_k sc3_kmeans sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.			13		sc3-scripts		To update	UseGalaxy.eu7
suite_pyscenic	0.12.1	pyscenic_aucell pyscenic_binarize pyscenic_ctx pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/			0				To update
suite_monocle3	0.1.4	monocle3_create monocle3_diffExp monocle3_learnGraph monocle3_orderCells monocle3_partition monocle3_plotCells monocle3_preprocess monocle3_reduceDim monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.			5481		monocle3-cli		To update	UseGalaxy.eu9 UseGalaxy.or9
suite_garnett	0.2.8	garnett_check_markers garnett_classify_cells garnett_get_feature_genes garnett_get_std_output garnett_train_classifier garnett_transform_markers update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8			27		garnett-cli		To update	UseGalaxy.eu7
suite_dropletutils	1.0.4	dropletutils_empty_drops dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3			2813		dropletutils-scripts		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
suite_decoupler	1.4.0+galaxy3	score_genes_aucell decoupler_pathway_inference decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities			122		decoupler		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
suite_ebi_expression_atlas	v0.0.2+galaxy2	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home			1738		wget		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
suite_human_cell_atlas_tools	v0.0.4+galaxy0	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects			559		hca-matrix-downloader		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
suite_celltypist	1.6.3+galaxy1	celltypist_predict	celltypist - Automated cell type annotation			0		celltypist		To update
suite_cell_types_analysis	1.1.1	ct_build_cell_ontology_dict ct_check_labels ct_combine_tool_outputs ct_downsample_cells ct_get_consensus_outputs ct_get_empirical_dist ct_get_tool_perf_table ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis			9		cell-types-analysis		To update	UseGalaxy.eu6
salmon_kallisto_mtx_to_10x	0.0.1+galaxy6	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data			1139		scipy		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
fastq_utils	0.25.1+galaxy0	fastq_filter_n fastq_trim_poly_at	Set of tools for handling fastq files			0		fastq_utils		To update
fastq_quality_trimmer	0.0.14+galaxy0	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality			0		fastx_toolkit		To update
fastq_pair	1.0+galaxy0	fastq_pair	Paired-end fastq pairer			0		fastq-pair		To update
gtf2gene_list	1.52.0+galaxy0	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.			3734		atlas-gene-annotation-manipulation		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
atlas_fastq_provider	0.4.4	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.			0		atlas-fastq-provider		To update
droplet_barcode_plot	1.6.1+galaxy2	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC			1752		scxa-plots		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
smithsonian_volcanoes	0.1.0	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database			0		python		To update
shift_longitudes	0.1.0	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees			80		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
psy_maps	1.3.1	psy_maps	Visualization of regular geographical data on a map with psyplot			557		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
mean_per_zone	0.2.0	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file			25		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
ctsm_fates	2.0	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model			426		fates-emerald		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
cds_essential_variability	0.2.0	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability			336		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
eodie	1.0.2	eodie	Earth Observation Data Information Extractor			45		eodie		To update	UseGalaxy.cz1 UseGalaxy.eu1
climate_stripes	1.0.2	climate_stripes	Create climate stripes from a tabular input file			482		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
cesm	2.1.3	cesm	Community Earth System Model (CESM)			14		cesm		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
cdo	2.0.0	cdo_info cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.			228				To update	UseGalaxy.cz2 UseGalaxy.eu2
cads	0.1.0	cads	Copernicus Atmosphere Data Store (ADS)			52		python		To update	UseGalaxy.cz1 UseGalaxy.eu1
c3s	0.3.0	c3s	Copernicus Climate Change Service (C3S)			459		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
zoo_project_ogc_api_processes	0.1.0	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.			26		r-base		To update	UseGalaxy.eu1
xmlstarlet	1.6.1	xmlstarlet	Tool to convert a xml file from one metadata standard to another			103		xmlstarlet		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
xarray_import_data	0.1.0	xarray_import_data	A data import tool for opening OPeNDAP datasets and storing as netCDF files.			0		xarray		To update	UseGalaxy.eu1
vigiechiro	0.1.1	vigiechiro_bilanenrichipf vigiechiro_bilanenrichirp vigiechiro_idcorrect_2ndlayer vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.			15636				To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4
terrabyte_ogc_api_processes	0.1.0	terrabyte_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/).			10		r-base		To update	UseGalaxy.eu1
stoceps	0.0.2	stoceps_filteringsp stoceps_glm stoceps_glm_group stoceps_maketablecarrer stoceps_trend_indic	Tools to analyse STOC data.			338				To update	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5
srs_tools	0.0.1	srs_diversity_maps srs_global_indices srs_process_data srs_spectral_indices srs_pca srs_preprocess_s2 srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2			315		r-base		To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.or4
spocc_occ	1.2.2	spocc_occ	Get species occurences data			915				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
sdmpredictors	0.2.15	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.			3		r-base		To update	UseGalaxy.eu1
retrieve_bold	1.3.0	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers			10		r-base		To update	UseGalaxy.eu1
regionalgam	1.5	regionalgam_ab_index regionalgam_autocor_acf regionalgam_flight_curve regionalgam_glmmpql regionalgam_gls_adjusted regionalgam_gls regionalgam_plot_trend				546		r-mgcv		To update	UseGalaxy.be6 UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.no7
ogcProcess_otb_meanShiftSmoothing	1.0	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.			57		r-base		To update	UseGalaxy.eu1
ogcProcess_otb_bandmath	1.0	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.			99		r-base		To update	UseGalaxy.eu1
ocean_neural_network	0.9.3	bgc_canyon_b	Robust Estimation of Open Ocean CO2 Variables and Nutrient Concentrations From T, S, and O2 Data Using Bayesian Neural Networks			0		r-base		To update	UseGalaxy.eu1
ocean_data_view_manager	2.1	tool_biogeochemical_calibration tool_odv tool_odv_history	The tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet in an automatic way.			0				To update	UseGalaxy.eu3
ocean	0.1.15	argo_getdata copernicusmarine divand_full_analysis	Access, process, and visualise oceanographic data for the Earth System			99		copernicusmarine		To update	UseGalaxy.eu3
obisindicators	0.0.2	obisindicators obis_data	Compute biodiveristy indicators for marine data from obis			374		r-base		To update	UseGalaxy.cz1 UseGalaxy.eu2 UseGalaxy.fr1 UseGalaxy.or1
medenv	0.1.0	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa			34		pandas		To update	UseGalaxy.eu1
marine_omics	0.9.3.5	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data			109		sanntis		To update	UseGalaxy.eu1 UseGalaxy.or1
Make data paper sketches from EML	0.1.0+galaxy0	data_paper_from_EML	This tool derived from the R Shiny App MetaShRIMPS <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents.			24		r-base		To update	UseGalaxy.eu1
interpolation	1.0	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file			70		r-getopt		To update	UseGalaxy.eu1
hirondelle_crim_ogc_api_processes	0.2.0	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.			236		r-base		To update	UseGalaxy.eu1
gdal	3.0.0	gdal_gdal_merge gdal_gdal_translate gdal_gdaladdo gdal_gdalbuildvrt gdal_gdalinfo gdal_gdalwarp gdal_ogr2ogr gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.			1511				To update	UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr8 UseGalaxy.no8
earth	0.1.0	landcover_subindicator	Access, process, visualise oceanographic data for the Earth System			2		numpy		To update	UseGalaxy.eu1
xarray	2022.3.0	timeseries_extraction xarray_coords_info xarray_mapplot xarray_metadata_info xarray_netcdf2netcdf xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.			6481		xarray		To update	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr5 UseGalaxy.no2 UseGalaxy.or2
data_exploration	0.0.0	tool_anonymization ecology_homogeneity_normality ecology_beta_diversity ecology_link_between_var ecology_presence_abs_abund ecology_stat_presence_abs	Explore data through multiple statistical tools			1252		r-tangles		To update	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6
consalign	1.0.0	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences			5860		r-bioseq		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
champ_blocs	0.0.0	cb_dissim cb_ivr cb_div	Compute indicators for turnover boulders fields			216		r-base		To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3
bgc_ocean	3.0	harmonize_insitu_to_netcdf	Process in-situ and biogechemical oceanographic Argo or Glider data for the Earth System			19				To update	UseGalaxy.eu1
aquainfra_ogc_api_processes	0.7.0	aquainfra_ogc_api_processes	Wrapper for OGC API Processes developed in the AquaINFRA project.			257		r-base		To update	UseGalaxy.eu1
aquainfra_importer	1.0	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.			277				To update	UseGalaxy.eu1
ab1fastq	1.20.0	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files			62357		bioconductor-sangerseqr		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
WormsMeasurements	0.1.2	WormsMeasurements	This tool uses WoRMS (World Register of Marine Species) to add measurement values to a dataset based on scientific names.			0		r-base		To update	UseGalaxy.eu1
PyloIndex	1.0	phylo_index	Tools to computes the phylodiversity index.			0		r-phyloregion		To update	UseGalaxy.eu1
PylOccuMatcher	1.0	phylogenetic_occupancy_matcher	Tools to matches phylogenetic data with occupancy data.			0		r-phyloregion		To update	UseGalaxy.eu1
pampa	0.0.2	pampa_communitymetrics pampa_presabs pampa_glmcomm pampa_glmsp pampa_plotglm	Tools to compute and analyse biodiversity metrics			2214				To update	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no4 UseGalaxy.or5
Geometric means (Dead wood)	0.1.0+galaxy0	Map_shp Mean_geom bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).			89		r-base		To update	UseGalaxy.eu3 UseGalaxy.fr3
EstimEndem	0.1.1+galaxy0	estimate_endem	Tools to estimates the endemism of each cell in a spatial grid.			0		r-phyloregion		To update	UseGalaxy.eu1
ecoregionalization	0.1.2+galaxy0	ecoregion_brt_analysis ecoregion_GeoNearestNeighbor ecoregion_cluster_estimate ClaraGuess ecoregion_clara_cluster ecoregion_eco_map indicspecies ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.			642		r-base		To update	UseGalaxy.cz5 UseGalaxy.eu8 UseGalaxy.fr5
emlassemblyline	0.1.0+galaxy0	annotations_template eal_table_template eal_templates eml2eal eml_validate entities_template geo_cov_template makeeml raster_template taxo_cov_template vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa			618		r-base		To update	UseGalaxy.cz2 UseGalaxy.eu11 UseGalaxy.fr9
CRSConverter	1.1	crsconverter	Tools to transforms geographical vector data to a specified coordinate reference system.			0		r-sf		To update	UseGalaxy.eu1
yac_clipper	2.5.1	yac	Clips 3' adapters for small RNA sequencing reads.			0		python		To update
xpore	2.1+galaxy0	xpore_dataprep xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing			0		xpore		To update
wisecondorx	1.2.9	wisecondorx_npz_converter wisecondorx_predict wisecondorx_reference_builder	WisecondorX			0		wisecondorx		Up-to-date
varscan_vaf	0.1	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.			0		python		To update
tarfast5	0.6.1	tarfast5	produces a tar.gz archive of fast5 sequence files			0		pigz		To update	UseGalaxy.no1
sr_bowtie_dataset_annotation	2.8	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.			0		bowtie		To update
sr_bowtie	2.3.1	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads	Microbiology Biology		98	sr_bowtie	bowtie		To update
snvtocnv	3.0.0+galaxy1	sequenzaindex snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza			0		sequenza-utils		To update
small_rna_signatures	3.4.2	overlapping_reads signature	Computes the tendency of small RNAs to overlap with each other.			0		pysam		To update
small_rna_maps	3.1.1	small_rna_maps	Generates small read maps from alignment BAM files			0		numpy		To update
small_rna_clusters	1.3.0	small_rna_clusters	clusters small rna reads in alignment BAM files			0		pysam		To update
sequence_format_converter	2.2.0	sequence_format_converter	various fasta to tabular conversions			0		python		To update
sashimi_plot	0.1.1	sashimi_plot	Generates a sashimi plot from bam files.			0		python		To update
sambamba	0.7.1+galaxy1	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM			836		sambamba		To update	UseGalaxy.or1
rsem		extract_transcript_to_gene_map_from_trinity purgegtffrommultichromgenes rsembowtie2 rsembowtie	transcript quantification from RNA-Seq data			606		rsem		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
repenrich2	2.31.1	edger-repenrich2 repenrich2	Repeat element profiling using bowtie2 aligner			0				To update
repenrich	2.31.1	edger-repenrich repenrich	Repeat element profiling			1935				To update	UseGalaxy.or2
probecoverage	0.22.0	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets			0		pysam		To update
pindel	0.2.5b9	pindel	Pindel detects genome-wide structural variation.			0		pindel		Up-to-date
pathifier	1.40.0	pathifier	pathifier			257		bioconductor-pathifier		To update	UseGalaxy.cz1 UseGalaxy.eu1
oases	1.4.0	oasesoptimiserv	Short read assembler			0		oases		To update
mutational_patterns	3.12.0	mutational_patterns	Mutational patterns and signatures in base substitution catalogs			0		bioconductor-mutationalpatterns		To update
mircounts	1.6	mircounts	Generates miRNA count lists from read alignments to mirBase.			1646		tar		To update	UseGalaxy.or1
mapping_quality_stats	0.22.0	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file			0		r-optparse		To update
manta	1.6	manta	Structural variant and indel caller for mapped sequencing data			568		manta		To update	UseGalaxy.cz1 UseGalaxy.eu1
lumpy_sv	1.3	lumpy	Find structural variations			0		lumpy-sv		To update
lumpy_smoove	0.2.8+galaxy1	lumpy_smoove vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow			0		svtyper		To update
justgzip	2.8+galaxy0	justgzip	Compress fastq sequence files			20		pigz		To update
justdiff	3.10+galaxy0	justdiff	Unix diff			0		diffutils		To update
high_dim_heatmap	3.1.3+galaxy0	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps			0		r-gplots		To update
guppy_basecaller	6.5.7+galaxy0	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies			7				To update
gsc_signature_score	2.3.9+galaxy1	signature_score	Compute signature scores from single cell RNAseq data		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
gsc_scran_normalize	1.28.1+galaxy1	scran_normalize	Normalize raw counts using scran		RNA-Seq analysis Clustering Visualisation Expression analysis	508	galaxy_single_cell_suite	bioconductor-scran		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
gsc_mannwhitney_de	4.1.3+galaxy1	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
gsc_high_dimensions_visualisation	4.3+galaxy1	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
gsc_gene_expression_correlations	4.3.1+galaxy1	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
gsc_filter_genes	4.3.1+galaxy1	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
gsc_filter_cells	4.3.1+galaxy1	filter_cells	Filter single cell RNAseq data on library depth and number of detected genes		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
gsc_center_scale	4.3.1+galaxy1	center_scale	Center or scale (standardize) data		RNA-Seq analysis Clustering Visualisation Expression analysis	0	galaxy_single_cell_suite	r-optparse		To update
get_reference_fasta	0.3.2	get_fasta_reference	Obtain reference genome sequence.			0				To update
gatk4	4.1.7.0	filtermutectcalls mergemutectstats mutect2	Find somatic variations			0		gatk4		To update
fishertest	2.32.0+galaxy0	fishertest	Fisher's exact test on two-column hit lists.			0		bioconductor-qvalue		To update
fetch_fasta_from_ncbi	3.1.0	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers			5		urllib3		To update
ez_histograms	3.4.4	ez_histograms	ggplot2 histograms and density plots	Ecology	Data analysis Statistical calculation Visualisation	0	ez_histograms	r-ggplot2		To update
embl2fa	0.2	embl2fa	Converts EMBL flat format to fasta format			0				To update
deseq2_normalization	1.40.2+galaxy1	deseq2_normalization	Normalizes gene hitlists			0		bioconductor-deseq2		To update
cpm_tpm_rpk	0.6.0	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts			0		r-optparse		To update
concatenate_multiple_datasets	1.4.3	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.			15438				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
cherry_pick_fasta	4.1	cherry_pick_fasta	Pick fasta sequence with specific header content			0		python		To update
cap3	2.0.1	cap3	cap3 wrapper			19100		cap3		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
blastx_to_scaffold	1.1.1	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs			0		python		To update
blastparser_and_hits	2.7.1	BlastParser_and_hits	Parse blast outputs and compile hits			8		python		To update
blast_unmatched	1.0.1	blast_unmatched	Extract unmatched query sequences from blast			0		python		To update
blast_to_scaffold	1.1.0	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs			8		python		To update
bigwig_to_wig	3+galaxy0	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format			0		ucsc-bigwiginfo		To update
bigwig_to_bedgraph	377+galaxy1	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format			7955		ucsc-bigwigtobedgraph		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
bamparse	4.1.1	bamparse	Generates hit count lists from bam alignments.			0		pysam		To update
artbio_bam_cleaning	1.10+galaxy0	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis			0		samtools		To update
vmd			vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations			0				To update
openmm	1.8.1	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.			1233		pdbfixer		To update	UseGalaxy.cz1 UseGalaxy.eu1
mdtraj	1.9.7	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories			99		mdtraj		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
md_converter	1.9.9	md_slicer	A tool for slicing trajectory files using MDTraj.			666		mdtraj		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
md_converter	1.9.7	md_converter	A tool for interconverting between different MD structure and trajectory file formats.			29245		mdtraj		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
mdanalysis	1.0.0	mdanalysis_angle mdanalysis_dihedral mdanalysis_distance mdanalysis_endtoend mdanalysis_extract_rmsd mdanalysis_hbonds mdanalysis_cosine_analysis mdanalysis_ramachandran_protein mdanalysis_ramachandran_plot mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations			4201		mdanalysis		To update	UseGalaxy.be1 UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.no10 UseGalaxy.or5
gromacs	2022	gmx_check gmx_editconf gmx_energy gmx_get_builtin_file gmx_rg gmx_makendx gmx_merge_topology_files gmx_em gmx_restraints gmx_rmsd gmx_rmsf gmx_setup gmx_sim gmx_solvate gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.			214953		gromacs		To update	UseGalaxy.be6 UseGalaxy.cz15 UseGalaxy.eu15 UseGalaxy.no9 UseGalaxy.or8
freeenergy			Free energy tools of BRIDGE.			0				To update
topologyeditors	0	gromacs_modify_topology gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.			88		python		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.or2
packmol	18.169.1	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations			722		packmol		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
ambertools	21.10	ambertools_acpype acpype_Amber2Gromacs ambertools_antechamber mmpbsa_mmgbsa ambertools_parmchk2 parmconv tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.			46482		ambertools		To update	UseGalaxy.be1 UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.no5 UseGalaxy.or2
biomoldyn	1.5.2	biomd_neqgamma fastpca biomd_extract_clusters biomd_rmsd_clustering	Tools for MD analysis			1107		scipy		To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no3 UseGalaxy.or4
biobb_pytorch	4.2.1	biobb_pytorch_apply_mdae biobb_pytorch_train_mdae	biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library.			0		biobb_pytorch		To update
bio3d	2.4_1	bio3d_dccm bio3d_pca bio3d_rmsd bio3d_rmsf bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.			16285		r-bio3d		To update	UseGalaxy.be4 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5 UseGalaxy.or4
zeiss_lmd_converter	2.0.4	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems			8		shapely		To update	UseGalaxy.eu1
validate_fasta_database	0.1.5	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.			254		validate-fasta-database		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
uniprotxml_downloader	2.5.0	uniprotxml_downloader	Download UniProt proteome in XML or fasta format			2631		requests		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
unipept	6.2.4+galaxy0	unipept	Unipept retrieves metaproteomics information	Proteomics Proteogenomics Biodiversity Workflows	Prediction and recognition Visualisation	7083	unipept	python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
translate_bed_sequences	0.2.0	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column			69		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
spectrast2tsv	0.1.0	gp_spectrast2tsv	Filter from spectraST files to swath input files			0		msproteomicstools		To update
spectrast2spectrast_irt	0.1.0	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files			0		msproteomicstools		To update
sixgill	0.2.4	sixgill_build sixgill_filter sixgill_makefasta sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS			316		sixgill		Up-to-date	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no4
scaffold	0.1.0	scaffold scaffold_export				0		scaffold		To update
regex_find_replace	1.0.3	regex1 regexColumn1	Use python regular expressions to find and replace text			117062		python		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
rawtools		rawtools	Raw Tools			660		rawtools		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
qupath_roi_splitter	0.3.2	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type			181		geojson		To update	UseGalaxy.cz1 UseGalaxy.eu1
quantwiz_iq	2.0	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ			32		quantwiz-iq		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
quantp	1.1.2	quantp	Correlation between protein and transcript abundance			242		r-data.table		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
pyteomics	4.4.1	mztab2tsv	Tools using the pyteomics library	Proteomics Proteomics experiment	Protein identification	92	pyteomics	pyteomics		To update	UseGalaxy.cz1 UseGalaxy.eu1
pyprophet	2.1.4	pyprophet_export pyprophet_merge pyprophet_peptide pyprophet_protein pyprophet_score pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.			3435		pyprophet		To update	UseGalaxy.be5 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.no6 UseGalaxy.or5
ptxqc	1.1.2	maxquant_ptxqc	Quality control reports for MaxQuant results	Proteomics	Validation	0	ptxqc	r-ptxqc		To update
psm_validation	1.0.3	psmvalidator	Validate PSM from Ion Fragmentation			20				To update	UseGalaxy.cz1 UseGalaxy.eu1
psm_eval	0.1.0	psm_eval				0		binaries_for_psm_eval		To update
protxml_to_xls	0.1.0	protxml_to_xls				0		trans_proteomic_pipeline		To update
proteore_venn_diagram	2021.06.08	proteore_venn_diagram	ProteoRE JVenn Diagram			15		python		To update
proteomiqon_psmstatistics	0.0.8	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.			694		proteomiqon-psmstatistics		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_psmbasedquantification	0.0.8	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.			604		proteomiqon-psmbasedquantification		To update	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_proteininference	0.0.7	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.			89		proteomiqon-proteininference		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_peptidespectrummatching	0.0.7	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.			686		proteomiqon-peptidespectrummatching		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_peptidedb	0.0.7	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.			96		proteomiqon-peptidedb		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_mzmltomzlite	0.0.8	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.			722		proteomiqon-mzmltomzlite		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.			8		proteomiqon-labelfreeproteinquantification		To update	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_labeledproteinquantification	0.0.1	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.			16		proteomiqon-labeledproteinquantification		To update	UseGalaxy.cz1 UseGalaxy.eu1
proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.			372		proteomiqon-joinquantpepionswithproteins		To update	UseGalaxy.cz1 UseGalaxy.eu1
translate_bed	0.1.0	translate_bed	Translate BED transcript CDS or cDNA in 3 frames			2077				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
retrieve_ensembl_bed	0.1.0	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format			0				To update
proteinpilot	0.1	convert_windows_newlines proteinpilot proteinpilot_group_extractor proteinpilot_tabular proteinpilot_xml				0				To update
psm_to_sam	1.3.2.1	PSMtoSAM	PSM to SAM			0		r-base		To update	UseGalaxy.fr1
custom_pro_db_annotation_data_manager			CustomProDB Annotation			0				To update
custom_pro_db	1.22.0	custom_pro_db	CustomProDB			2661		bioconductor-rgalaxy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
pmd_fdr	1.4.0	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS			0		r-base		To update
hirieftools	1.3	calc_delta_pi pi_db_split pi_dbspec_align	HiRIEF tools			0		python		To update
percolator	3.5	batched_set_list_creator percolator percolator_input_converters pout2mzid	Percolator			1629		percolator		To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no4 UseGalaxy.or4
pepxml_to_xls			Convert PepXML to Tabular			0				To update
peptideshaker		fasta_cli ident_params peptide_shaker search_gui	PeptideShaker and SearchGUI			23289		searchgui		To update	UseGalaxy.be2 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no2 UseGalaxy.or4
peptide_genomic_coordinate	1.0.0	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files			660		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
pepquery2	2.0.2	pepquery2 pepquery2_index pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation			1749		pepquery		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.or1
pepquery	1.6.2	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.			7435		pepquery		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
pep_pointer	0.1.3+galaxy1	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.			753		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
reactome_pathwaymatcher		reactome_pathwaymatcher	Reactome Pathway Matcher			258		pathwaymatcher		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
openms	3.1	AccurateMassSearch AssayGeneratorMetabo BaselineFilter CVInspector ClusterMassTraces ClusterMassTracesByPrecursor CometAdapter ConsensusID ConsensusMapNormalizer DTAExtractor DatabaseFilter DatabaseSuitability DeMeanderize DecoyDatabase Digestor DigestorMotif EICExtractor ERPairFinder Epifany ExternalCalibration FalseDiscoveryRate FeatureFinderCentroided FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMRM FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMultiplex FeatureLinkerLabeled FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FileConverter FileFilter FileInfo FileMerger FuzzyDiff GNPSExport HighResPrecursorMassCorrector IDConflictResolver IDExtractor IDFileConverter IDFilter IDMapper IDMassAccuracy IDMerger IDPosteriorErrorProbability IDRTCalibration IDRipper IDScoreSwitcher IDSplitter InternalCalibration IsobaricAnalyzer JSONExporter LuciphorAdapter MRMMapper MRMPairFinder MRMTransitionGroupPicker MSFraggerAdapter MSGFPlusAdapter MSstatsConverter MapAlignerIdentification MapAlignerPoseClustering MapAlignerSpectrum MapAlignerTreeGuided MapNormalizer MapRTTransformer MapStatistics MascotAdapter MascotAdapterOnline MassCalculator MassTraceExtractor MetaProSIP MetaboliteSpectralMatcher MultiplexResolver MzMLSplitter MzTabExporter NoiseFilterGaussian NoiseFilterSGolay NovorAdapter NucleicAcidSearchEngine OpenMSDatabasesInfo OpenMSInfo OpenPepXL OpenPepXLLF OpenSwathAnalyzer OpenSwathAssayGenerator OpenSwathChromatogramExtractor OpenSwathConfidenceScoring OpenSwathDIAPreScoring OpenSwathDecoyGenerator OpenSwathFeatureXMLToTSV OpenSwathFileSplitter OpenSwathMzMLFileCacher OpenSwathRTNormalizer OpenSwathRewriteToFeatureXML OpenSwathWorkflow PSMFeatureExtractor PeakPickerHiRes PeakPickerIterative PeakPickerWavelet PeptideIndexer PercolatorAdapter PhosphoScoring PrecursorMassCorrector ProteinInference ProteinQuantifier ProteinResolver QCCalculator QCEmbedder QCExporter QCExtractor QCImporter QCMerger QCShrinker QualityControl RNADigestor RNAMassCalculator RNPxlSearch RNPxlXICFilter SageAdapter SeedListGenerator SemanticValidator SequenceCoverageCalculator SimpleSearchEngine SiriusAdapter SpecLibCreator SpecLibSearcher SpectraFilterBernNorm SpectraFilterMarkerMower SpectraFilterNLargest SpectraFilterNormalizer SpectraFilterParentPeakMower SpectraFilterScaler SpectraFilterSqrtMower SpectraFilterThresholdMower SpectraFilterWindowMower SpectraMerger SpectraSTSearchAdapter StaticModification TICCalculator TOFCalibration TargetedFileConverter TextExporter TriqlerConverter XFDR XMLValidator XTandemAdapter	OpenMS Suite for LC/MS data management and analyses			113988		openms		To update	UseGalaxy.be18 UseGalaxy.cz141 UseGalaxy.eu144 UseGalaxy.no124 UseGalaxy.or34
mz_to_sqlite	2.1.1+galaxy0	mz_to_sqlite	Creates a SQLite database for proteomics data	Proteomics Biological databases	Conversion Peptide database search	1239	mztosqlite	mztosqlite		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
mt2mq	1.1.0	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome			276		r-tidyverse		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
msstatstmt	2.0.0	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling			1410		bioconductor-msstatstmt		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
msstatstmt	4.0.0	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	Proteomics Proteomics experiment Protein expression	Spectrum calculation Tag-based peptide identification Differential protein expression profiling	5259	msstatstmt	bioconductor-msstats		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
msms_extractor	1.0.0	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.			121		proteowizard		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
msgfplus	0.5	msgfplus	MSGF+			810		msgf_plus		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
msconvert	3.0.20287	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	Proteomics Proteomics experiment	Filtering Formatting	75864	msconvert			To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
mqppep	0.1.19	mqppep_anova mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA			13		bioconductor-preprocesscore		To update	UseGalaxy.cz2 UseGalaxy.eu2
morpheus	288	morpheus	Morpheus MS Search Application	Proteomics	Peptide database search	1197	morpheus	morpheus		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
proteomics_moff	2.0.3	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.			944		moff		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
mgf_formatter	1.0.0	mgf_formatter				0		mgf-formatter		Up-to-date
metaquantome	2.0.2	metaquantome_db metaquantome_expand metaquantome_filter metaquantome_sample metaquantome_stat metaquantome_viz	quantitative analysis of microbiome taxonomy and function	Proteomics Metatranscriptomics Microbial ecology Proteomics experiment Metagenomics	Principal component visualisation Visualisation Functional clustering Query and retrieval Differential protein expression analysis Heat map generation Quantification Indexing Filtering Statistical inference	4904	metaQuantome	metaquantome		Up-to-date	UseGalaxy.be6 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.no6 UseGalaxy.or6
metanovo	1.9.4	metanovo	Produce targeted databases for mass spectrometry analysis.	Proteomics Microbial ecology Metagenomics Proteomics experiment Small molecules	Target-Decoy de Novo sequencing Tag-based peptide identification Protein identification Expression analysis	4956	metanovo	metanovo		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
metagene_annotator	1.0	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	Genomics Model organisms Data submission, annotation and curation	Sequence annotation	1198	metageneannotator	metagene_annotator		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
meta_proteome_analyzer	2.0.0	meta_proteome_analyzer	MetaProteomeAnalyzer			142		mpa-portable		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
maxquant	2.0.3.0	maxquant maxquant_mqpar	wrapper for MaxQuant	Proteomics experiment Proteomics Statistics and probability	Imputation Visualisation Protein quantification Statistical calculation Standardisation and normalisation Heat map generation Clustering Principal component plotting	14814	maxquant	maxquant		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
map_peptides_to_bed	0.2	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser			46		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
MALDIquant	1.22.0	maldi_quant_peak_detection maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.			5040		r-base		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
ltq_iquant_cli						0				To update
lfq_protein_quant	1.0	lfq_protein_quant	Enable protein summarisation and quantitation			116		bioconductor-msnbase		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
iedb_netmhcpan	4.1+galaxy0	iedb_netmhciipan iedb_netmhcpan	Predict binding of peptides to any MHC or MHC II molecule of known sequence using artificial neural networks			0				To update	UseGalaxy.eu2
idconvert		idconvert	Convert mass spectrometry identification files on linux or MacOSX			277		proteowizard		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
hardklor	2.30.1+galaxy1	hardklor kronik	Hardklör			111		hardklor		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2
gffcompare_to_bed	0.2.1	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED			4001		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
fragpipe	20.0	fragpipe	Data analysis for mass spectrometry-based proteomics.			210		fragpipe		To update	UseGalaxy.eu1 UseGalaxy.or1
flashlfq	1.0.3.1	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	Proteomics experiment Proteomics	Label-free quantification	911	flashlfq	flashlfq		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
filter_by_fasta_ids	2.3	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences			169301		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
feature_alignment	0.11.0	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy			18		msproteomicstools		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
fastg2protlib	1.0.2	fastg2protlib-peptides fastg2protlib-validate	Generate FASTA from FASTG			29				To update	UseGalaxy.cz2 UseGalaxy.eu2
fasta_merge_files_and_filter_unique_sequences	1.2.0	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together			78421		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
encyclopedia	1.12.34	encyclopedia_encyclopedia encyclopedia_fasta_to_prosit_csv encyclopedia_library_to_blib encyclopedia_prosit_csv_to_library encyclopedia_quantify encyclopedia_searchtolib encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis			857		encyclopedia		To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.or4
eggnog_mapper	2.1.8	eggnog_mapper eggnog_mapper_annotate eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	Metagenomics Phylogeny Transcriptomics Workflows Sequence analysis	Homology-based gene prediction Genome annotation Fold recognition Information extraction Query and retrieval	128641	eggnog-mapper-v2	eggnog-mapper		To update	UseGalaxy.be1 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
data_manager_eggnog_mapper_abspath			download eggnog data for eggnog-mapper			0				To update
data_manager_eggnog_mapper			downloads eggnog data for eggnog-mapper			0				To update
directag_and_tagrecon						0				To update
digestdb	0.1.0	digestdb				0		trans_proteomic_pipeline		To update
diffacto	1.0.6	diffacto	Diffacto comparative protein abundance estimation			11		diffacto		To update	UseGalaxy.cz1 UseGalaxy.eu1
diapysef	0.3.5.0	diapysef	diapysef is a convenience package for working with DIA-PASEF data			585		diapysef		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
diann	1.8.1	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.			351				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
dialignr	1.2.0	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.			40		bioconductor-dialignr		To update	UseGalaxy.cz1 UseGalaxy.eu1
dia_umpire	2.1.3	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics			188		dia_umpire		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
decoyfasta			Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.			0				To update
dbbuilder	0.3.4	dbbuilder	Protein Database Downloader			8363		wget		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
cardinal	3.4.3	cardinal_classification cardinal_colocalization cardinal_combine cardinal_data_exporter cardinal_filtering cardinal_mz_images cardinal_preprocessing cardinal_quality_report cardinal_segmentations cardinal_single_ion_segmentation cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets			59499		bioconductor-cardinal		To update	UseGalaxy.be9 UseGalaxy.cz11 UseGalaxy.eu11 UseGalaxy.fr11 UseGalaxy.no9 UseGalaxy.or9
calisp	3.0.13	calisp	Calgary approach to isotopes in proteomics			223		calisp		To update	UseGalaxy.cz1 UseGalaxy.eu1
bumbershoot	3.0.21142	idpqonvertEmbedder idpassemble idpqonvert idpquery myrimatch				1439		bumbershoot		To update	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5
blast_plus_remote_blastp	2.6.0	blast_plus_remote_blastp	NCBI BLAST+ with -remote option			0		blast		To update
bed_to_protein_map	0.2.0	bed_to_protein_map	Converts a BED file to a tabular list of exon locations			993		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
appendfdr	0.2.0	append_fdr				0				To update
thermo_raw_file_converter	1.3.4	thermo_raw_file_converter	Thermo RAW file converter	Proteomics Proteomics experiment Metabolomics	Conversion Filtering Peak detection	4213	ThermoRawFileParser	thermorawfileparser		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
vcfvcfintersect		vcfvcfintersect	Intersect two VCF datasets			1084461		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfsort		vcfsort	Sort VCF dataset by coordinate			28056		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfselectsamples		vcfselectsamples	Select samples from a VCF file			7655		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfrandomsample		vcfrandomsample	Randomly sample sites from VCF dataset			739		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfprimers		vcfprimers	Extract flanking sequences for each VCF record			1806		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfleftalign		vcfleftalign	Left-align indels and complex variants in VCF dataset			2080		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfhethom		vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.			6694		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfgenotypes		vcfgenotypes	Convert numerical representation of genotypes to allelic.			8101		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfgeno2haplo		vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles			4863		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfflatten		vcfflatten2	Removes multi-allelic sites by picking the most common alternate			1488		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcffixup		vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.			6682		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcffilter		vcffilter2	Tool for filtering VCF files			221503		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfdistance		vcfdistance	Calculate distance to the nearest variant.			3349		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfcommonsamples		vcfcommonsamples	Output records belonging to samples commong between two datasets.			2385		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfcombine		vcfcombine	Combine multiple VCF datasets			22714		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfcheck		vcfcheck	Verify that the reference allele matches the reference genome			3851		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfbreakcreatemulti		vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record			11403		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfbedintersect		vcfbedintersect	Intersect VCF and BED datasets			25498		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfannotategenotypes		vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.			2274		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfannotate		vcfannotate	Intersect VCF records with BED annotations			18316		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfallelicprimitives		vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines			35753		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcfaddinfo		vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.			10094		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcf2tsv		vcf2tsv	Converts VCF files into tab-delimited format			219658		vcflib		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
snpsift_genesets		snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome			1068		snpsift		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
snpsift_dbnsfp		snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani			478		snpsift		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
snpsift		snpSift_annotate snpSift_caseControl snpSift_extractFields snpSift_filter snpSift_int snpSift_rmInfo snpsift_vartype snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani			5705944		snpsift		To update	UseGalaxy.be8 UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr8 UseGalaxy.no8 UseGalaxy.or8
snpeff	5.2	snpEff snpEff_build_gb snpEff_databases snpEff_download snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox			332870		biopython		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or5
samtools	1.22					0		samtools		To update
kraken2	2.1.3	kraken2	Kraken2 for taxonomic designation.	Taxonomy Metagenomics Microbial ecology Microbiology	Taxonomic classification	618635	kraken2	kraken2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
kraken		kraken-filter kraken-mpa-report kraken-report kraken-translate kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	Taxonomy Metagenomics	Taxonomic classification	233430	kraken	kraken		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or5
tabular_to_fastq	1.1.5	tabular_to_fastq	Tabular to FASTQ converter			43794		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastqtofasta	1.1.5	fastq_to_fasta_python	FASTQ to FASTA converter			537669		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
fastq_trimmer	1.1.5	fastq_trimmer	FASTQ Trimmer by quality			108756		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_to_tabular	1.1.5	fastq_to_tabular	FASTQ to Tabular converter			57737		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_stats	1.1.5	fastq_stats	FASTQ Summary Statistics by column			91994		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_paired_end_splitter	1.1.5	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads			45492		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_paired_end_joiner	1.1.5	fastq_paired_end_joiner	FASTQ joiner on paired end reads			80045		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_paired_end_interlacer	1.1.5	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads			56567		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_paired_end_deinterlacer	1.1.5	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.			33865		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_masker_by_quality	1.1.5	fastq_masker_by_quality	FASTQ Masker by quality score			9032		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_manipulation	1.1.5	fastq_manipulation	Manipulate FASTQ reads on various attributes.			22838		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_groomer	1.1.5	fastq_groomer	Convert between various FASTQ quality formats.			1054852		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_filter	1.1.5	fastq_filter	Filter FASTQ reads by quality score and length			153167		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_combiner	1.1.5	fastq_combiner	Combine FASTA and QUAL into FASTQ			87437		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_trimmer	0.0.14	cshl_fastx_trimmer	Trim sequences			236326		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_reverse_complement	0.0.14	cshl_fastx_reverse_complement	Reverse-Complement			87246		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_renamer	0.0.14	cshl_fastx_renamer	Rename sequences			19621		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_quality_statistics	0.0.14	cshl_fastx_quality_statistics	Compute quality statistics			71021		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_nucleotides_distribution	0.0.14	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart			27103		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_collapser	0.0.14	cshl_fastx_collapser	Collapse sequences			298389		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_clipper	0.0.14	cshl_fastx_clipper	Clip adapter sequences			123635		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_barcode_splitter	0.0.14	cshl_fastx_barcode_splitter	Barcode Splitter			124269		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastx_artifacts_filter	0.0.14	cshl_fastx_artifacts_filter	Remove sequencing artifacts			29175		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_to_fasta	0.0.14	cshl_fastq_to_fasta	FASTQ to FASTA converter			168967		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_quality_filter	0.0.14	cshl_fastq_quality_filter	Filter by quality			187994		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_quality_converter	0.0.14	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)			11473		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_quality_boxplot	0.0.14	cshl_fastq_quality_boxplot	Draw quality score boxplot			62010		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_nucleotide_changer	0.0.14	cshl_fasta_nucleotides_changer	RNA/DNA converter.			6926		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_formatter	0.0.14	cshl_fasta_formatter	FASTA Width formatter			38903		fastx_toolkit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_clipping_histogram	0.0.14	cshl_fasta_clipping_histogram	Length Distribution chart			5786		fastx_toolkit		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
cuffquant	2.2.1	cuffquant	The Cuffquant tool			17093		cufflinks		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
cuffnorm	2.2.1	cuffnorm	The Cuffnorm tool			14558		cufflinks		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
cuffmerge	2.2.1	cuffmerge	Galaxy wrappers for the Cuffmerge tool.			74794		cufflinks		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
cufflinks	2.2.1	cufflinks	Galaxy wrappers for the Cufflinks tool.			398335		cufflinks		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
cuffdiff	2.2.1	cuffdiff	Galaxy wrappers for the Cuffdiff tool.			128374		cufflinks		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
cuffcompare	2.2.1	cuffcompare	Galaxy wrappers for the Cuffcompare tool.			27088		cufflinks		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
biotradis	1.4.5	bacteria_tradis tradis_essentiality tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	Mobile genetic elements Workflows	Sequence analysis	6465	biotradis	biotradis		Up-to-date	UseGalaxy.or3
bamtools	2.5.2	bamtools_split_mapped bamtools_split_paired bamtools_split_ref bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	Sequencing Data management Sequence analysis	Data handling Sequence alignment analysis	25660	bamtools	bamtools		To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr1 UseGalaxy.or3
bamtools_filter	2.5.2	bamFilter	Filter BAM datasets on various attributes using bamtools filter	Sequencing Data management Sequence analysis	Data handling Sequence alignment analysis	291365	bamtools	bamtools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
bamtools	2.5.2	bamtools	Operate on and transform BAM datasets in various ways using bamtools	Sequencing Data management Sequence analysis	Data handling Sequence alignment analysis	117874	bamtools	bamtools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
zerone	1.0	zerone	ChIP-seq discretization and quality control			96		zerone		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
yahs	1.2a.2	yahs	Yet Another Hi-C scaffolding tool			1929		yahs		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
xpath		xpath	XPath XML querying tool			237		perl-xml-xpath		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
winnowmap	2.03	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.			373		winnowmap		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
windowmasker	1.0	windowmasker_mkcounts windowmasker_ustat	Identify repetitive regions using WindowMasker			1902		blast		To update	UseGalaxy.eu2 UseGalaxy.or2
weblogo3	3.5.0	rgweblogo3	Sequence Logo generator for fasta	Nucleic acid sites, features and motifs Sequence analysis	Sequence cluster visualisation Sequence visualisation Sequence motif recognition	35167	weblogo	weblogo		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
simpleweather	0.1.2	simple_weather	provides simple weather in text format			0		curl		To update
vsnp	3.0.6	vsnp_add_zero_coverage vsnp_build_tables vsnp_determine_ref_from_data vsnp_get_snps vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.			0		pysam		To update
vsearch	2.8.3	vsearch_alignment vsearch_chimera_detection vsearch_clustering vsearch_dereplication vsearch_masking vsearch_search vsearch_shuffling vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	Metagenomics Sequence analysis	DNA mapping Chimera detection	76088	vsearch	vsearch		To update	UseGalaxy.be8 UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr8 UseGalaxy.no8 UseGalaxy.or8
volcanoplot	3.5.2	volcanoplot	Tool to create a Volcano Plot			110713		r-ggplot2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
virulign	1.1.1	virulign	A tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins.			0		virulign		Up-to-date
virhunter	1.0.0	virhunter	Deep Learning method for novel virus detection in sequencing data	Virology	Sequence classification	760	virhunter	numpy		To update	UseGalaxy.cz1 UseGalaxy.eu1
virheat	0.7.1	virheat	generates a heatmap of allele frequencies from vcf files			15	virheat	virheat		To update	UseGalaxy.eu1
virannot	1.2.0	virannot_blast2tsv virannot_otu virAnnot_rps2tsv	virAnnot wrappers	Metagenomics Virology Microbial ecology	Sequence annotation Sequence clustering Sequence cluster visualisation	285	virannot	biopython		To update	UseGalaxy.eu3 UseGalaxy.fr3
viralverify	1.1	viralverify	Contigs prediction as viral, chromosomal, plasmidic or uncertain.			0		viralverify		Up-to-date	UseGalaxy.fr1
vg	1.23.0	vg_convert vg_deconstruct vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods			479		vg		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3
verkko	1.3.1	verkko	Telomere-to-telomere assembly pipeline			130		verkko		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
velvetoptimiser	2.2.6+galaxy2	velvetoptimiser	Automatically optimize Velvet assemblies	Genomics Sequence assembly	Optimisation and refinement Sequence assembly	21631	velvetoptimiser	velvet		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
velvet		velvetg velveth	de novo genomic assembler specially designed for short read sequencing technologies	Sequence assembly	Formatting De-novo assembly	113927	velvet	velvet		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
velocyto	0.17.17	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.		RNA-Seq analysis Splicing analysis	235	velocyto	velocyto.py		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
vegan	2.4-3	vegan_diversity vegan_fisher_alpha vegan_rarefaction	an R package fo community ecologist	Ecology Phylogenetics Environmental science	Standardisation and normalisation Analysis	8041	vegan	r-vegan		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.no3 UseGalaxy.or3
vcfanno	0.3.7	vcfanno	Annotate VCF files	Genetic variation Data submission, annotation and curation	SNP annotation	1187	vcfanno	vcfanno		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
vcf2maf	1.6.21	vcf2maf	vcf2maf: Convert VCF into MAF			1498		vcf2maf		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
varvamp	1.2.2	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	Virology Probes and primers	PCR primer design	438	varvamp	varvamp		Up-to-date	UseGalaxy.eu1
varscan	2.4.3	varscan_copynumber varscan_mpileup varscan_somatic	VarScan is a variant caller for high-throughput sequencing data			33107		varscan		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
variant_analyzer	2.0.0	mut2read mut2sscs read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data			652		matplotlib		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.no3 UseGalaxy.or3
vardict_java	1.8.3	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs			387		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
vapor	1.0.3	vapor	Classify Influenza samples from raw short read sequence data	Whole genome sequencing Mapping Sequence assembly	Data retrieval De-novo assembly Read mapping	72539	vapor	vapor		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
valet		valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	Metagenomics Sequence assembly	Sequence assembly Sequence assembly visualisation	938	valet	valet		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
usher	0.2.1	usher_matutils usher	UShER toolkit wrappers	Phylogeny Evolutionary biology Cladistics Genotype and phenotype Phylogenomics	Classification Phylogenetic tree visualisation Phylogenetic inference (from molecular sequences)	1060	usher	usher		To update	UseGalaxy.cz2 UseGalaxy.eu2
upsetplot	1.4.0	rcx_upsetplot	Upset plot visualization tool using UpSetR			0		r-upsetr		To update
unicycler	0.5.1	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	Microbiology Genomics Sequencing Sequence assembly	Genome assembly Aggregation	203161	unicycler	unicycler		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
umi-tools	1.1.6	umi_tools_count umi_tools_dedup umi_tools_extract umi_tools_group umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	NGS Sequence sites, features and motifs Quality affairs	Sequencing quality control	96352	umi-tools	umi_tools		Up-to-date	UseGalaxy.be3 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or5
ucsc_wigtobigwig	482	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	Sequence analysis		8878	UCSC_Genome_Browser_Utilities	ucsc-wigtobigwig		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_nettoaxt	482	ucsc_nettoaxt	Convert net (and chain) to axt format.	Sequence analysis		8	UCSC_Genome_Browser_Utilities	ucsc-nettoaxt		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_netsyntenic	482	ucsc_netsyntenic	Add synteny info to a net dataset	Sequence analysis		23	UCSC_Genome_Browser_Utilities	ucsc-netsyntenic		Up-to-date	UseGalaxy.or1
ucsc_netfilter	482	ucsc_netfilter	Filter out parts of net	Sequence analysis		9	UCSC_Genome_Browser_Utilities	ucsc-netfilter		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_chainsort	482	ucsc_chainsort	Sort chains. By default sorts by score.	Sequence analysis		13	UCSC_Genome_Browser_Utilities	ucsc-chainsort		Up-to-date	UseGalaxy.or1
ucsc_chainprenet	482	ucsc_chainprenet	Remove chains that don't have a chance of being netted	Sequence analysis		13	UCSC_Genome_Browser_Utilities	ucsc-chainprenet		Up-to-date	UseGalaxy.or1
ucsc_chainnet	482	ucsc_chainnet	Make alignment nets out of chains	Sequence analysis		14	UCSC_Genome_Browser_Utilities	ucsc-chainnet		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_chainantirepeat	482	ucsc_chainantirepeat	Remove repeated chains	Sequence analysis		0	UCSC_Genome_Browser_Utilities	ucsc-chainantirepeat		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_axttomaf	482	ucsc_axtomaf	Convert dataset from axt to MAF format.	Sequence analysis		12	UCSC_Genome_Browser_Utilities	ucsc-axttomaf		Up-to-date	UseGalaxy.or1
ucsc_axtchain	482	ucsc_axtchain	Chain together genome alignments	Sequence analysis		11	UCSC_Genome_Browser_Utilities	ucsc-axtchain		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_twobittofa	482	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	Sequence analysis		1434	UCSC_Genome_Browser_Utilities	ucsc-twobittofa		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
maf_tools	482	ucsc_mafaddirows ucsc_mafcoverage ucsc_maffetch ucsc_mafFilter ucsc_maffrag ucsc_maffrags	Utilities for working with MAF (Multiple Alignment Format) files from UCSC			0		ucsc-mafaddirows		Up-to-date
ucsc_maftoaxt	482	maftoaxt	Convert dataset from MAF to axt format	Sequence analysis		9	UCSC_Genome_Browser_Utilities	ucsc-maftoaxt		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
ucsc_fatovcf	482	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	Sequence analysis		1351	UCSC_Genome_Browser_Utilities	ucsc-fatovcf		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
ucsc_fasplit	482	fasplit	faSplit is a tool to split a single FASTA file into several files	Sequence analysis		11964	UCSC_Genome_Browser_Utilities	ucsc-fasplit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ucsc_blat	482	ucsc_blat	Standalone blat sequence search command line tool	Sequence analysis	Sequence alignment	0	blat	ucsc-blat		Up-to-date
tximport	1.30.0	tximport	Wrapper for the Bioconductor package tximport	Transcriptomics Gene transcripts Workflows	Pathway or network analysis Formatting RNA-Seq analysis	9474	tximport	bioconductor-tximport		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tsne	0.0.2	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation			684		r-rtsne		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
tsebra	1.1.2.5	tsebra	This tool has been developed to combine BRAKER predictions.	Gene expression RNA-Seq Gene transcripts Model organisms	Homology-based gene prediction Alternative splicing prediction	43	tsebra	tsebra		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
trycycler	0.5.5	trycycler_cluster trycycler_consensus trycycler_partition trycycler_reconcile_msa trycycler_subsample	Trycycler toolkit wrappers	Sequence assembly DNA Human biology Whole genome sequencing Genomics	Genome assembly Sequence trimming Scaffold gap completion Sequence assembly validation	20075	trycycler	trycycler		Up-to-date	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.or5
trinotate	3.2.2	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	Gene expression Transcriptomics	Gene functional annotation	5478	trinotate	trinotate		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
trinity	2.15.1	trinity_abundance_estimates_to_matrix trinity_align_and_estimate_abundance trinity_analyze_diff_expr trinity_contig_exn50_statistic trinity_define_clusters_by_cutting_tree describe_samples trinity_filter_low_expr_transcripts trinity_gene_to_trans_map trinity_run_de_analysis trinity_samples_qccheck trinity_super_transcripts trinity trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics Gene expression Gene transcripts	Transcriptome assembly	122927	trinity	trinity		To update	UseGalaxy.be11 UseGalaxy.cz13 UseGalaxy.eu13 UseGalaxy.fr13 UseGalaxy.no12 UseGalaxy.or13
trimmomatic	0.39	trimmomatic	A flexible read trimming tool for Illumina NGS data			1529410		trimmomatic		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
trimal	1.5.0	trimal	Tool for automated alignment trimming	Sequence analysis Sequencing Sequence sites, features and motifs	Multiple sequence alignment	1072	trimal	trimal		Up-to-date	UseGalaxy.be1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
transtermhp		transtermhp	Finds rho-independent transcription terminators in bacterial genomes	Transcription factors and regulatory sites	Transcriptional regulatory element prediction	652	transtermhp	transtermhp		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
transit	3.2.3	gff_to_prot transit_gumbel transit_hmm transit_resampling transit_tn5gaps	TRANSIT	DNA Sequencing Mobile genetic elements	Transposon prediction	5375	transit	transit		To update	UseGalaxy.be2 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5 UseGalaxy.or5
transdecoder	5.5.0	transdecoder	TransDecoder finds coding regions within transcripts	Genomics Gene transcripts RNA-Seq Gene expression Sequence assembly Whole genome sequencing	Coding region prediction de Novo sequencing De-novo assembly	17172	TransDecoder	transdecoder		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
tracy	0.7.8	tracy_align tracy_assemble tracy_basecall tracy_decompose	A suite tools for basecalling, alignment, assembly and deconvolution of Sanger chromatograms using tracy.			3649		tracy		To update	UseGalaxy.cz4 UseGalaxy.eu4
tracegroomer	0.1.4	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.			52		tracegroomer		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
tooldistillator	1.0.0	tooldistillator tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	Microbiology Bioinformatics Sequence analysis	Data parsing	7899	tooldistillator	tooldistillator		Up-to-date	UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
tn93	1.0.15	tn93_readreduce tn93 tn93_cluster tn93_filter	Compute distances between sequences			4530		tn93		Up-to-date	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.or4
tetyper	1.1	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.			276		tetyper		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tetoolkit	2.2.3	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.			1246		tetranscripts		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tesseract	5.5.1	tesseract	Tesseract is an OCR engine with support for unicode and the ability to recognize more than 100 languages out of the box.			0		tesseract		To update	UseGalaxy.eu1
telescope_assign	1.0.3	telescope_assign	Single locus resolution of Transposable ELEment expression.	RNA-Seq Transcriptomics Mapping Gene transcripts Sequence assembly	Essential dynamics Sequence trimming RNA-Seq quantification Expression analysis Read mapping	0	Telescope-expression	telescope		Up-to-date
te_finder	1.0.1	te_finder	Transposable element insertions finder	Sequencing Mobile genetic elements Workflows Evolutionary biology Genetic variation	Genome indexing Variant calling PCR primer design	209	tefinder	samtools		To update	UseGalaxy.cz1 UseGalaxy.eu1
tbvcfreport	1.0.1	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)			16372		tbvcfreport		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
tbl2gff3	1.2	tbl2gff3	Table to GFF3			3195		bcbiogff		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
tb_variant_filter	0.4.0	tb_variant_filter	M. tuberculosis H37Rv VCF filter			65699		tb_variant_filter		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
tb-profiler	6.6.5	tb_profiler_collate tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.		Antimicrobial resistance prediction	27667	tb-profiler	tb-profiler		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
taxpasta	0.7.0	taxpasta	standardise taxonomic profiles	Taxonomy Metagenomics	Standardisation and normalisation Aggregation Formatting Conversion	90	taxpasta	taxpasta		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
taxonomy_krona_chart	2.7.1+galaxy0	taxonomy_krona_chart	Krona pie chart from taxonomic profile	Metagenomics	Visualisation	86851	krona	krona		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
taxonomy_filter_refseq	0.3.0	taxonomy_filter_refseq	Filter RefSeq by taxonomy			0		rust-ncbitaxonomy		To update
taxonkit	0.20.0	name2taxid profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	Taxonomy Biotechnology Ecology	Formatting Data retrieval	410	taxonkit	taxonkit		Up-to-date	UseGalaxy.eu2
tasmanian_mismatch	1.0.9	tasmanian_mismatch	Analysis of positional mismatches			276		tasmanian-mismatch		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
tag_pileup_frequency	1.0.2	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.			1034		openjdk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
table_compute	1.2.4	table_compute	Perform general-purpose table operations			257027		pandas		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
syri	1.7.1	syri	Synteny and Rearrangement Identifier	DNA polymorphism Sequence assembly DNA structural variation Mapping Sequencing	Haplotype mapping Variant calling Genotyping Sequence assembly Read mapping	7	SyRI	syri		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
syndiva	1.0	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.			30		clustalo		To update	UseGalaxy.cz1 UseGalaxy.eu1
swiftlink	1.0	swiftlink	Parallel MCMC Linkage Analysis			0		swiftlink		Up-to-date
structureharvester	0.6.94	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method			0		structureharvester		Up-to-date
structure	2.3.4	structure	for using multi-locus genotype data to investigate population structure.	Population genetics	Genetic variation analysis	3814	structure	structure		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
stringtie	2.2.3	stringtie stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	Transcriptomics RNA-Seq	Transcriptome assembly RNA-Seq analysis	655188	stringtie	stringtie		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
strelka	2.9.10	strelka_germline strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.			2593		strelka		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.or2
straindesign	3.2.2	straindesign_analyzing_model straindesign_reduce_model straindesign_simulate_deletion	Toolbox to optimize biological model			0		straindesign		To update
staramr	0.11.0	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.	Microbiology Public health and epidemiology Infectious disease	Antimicrobial resistance prediction	51323	staramr	staramr		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
star_fusion	0.5.4-3+galaxy1	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR			4813		star-fusion		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
stacks2	2.55	stacks2_clonefilter stacks2_cstacks stacks2_denovomap stacks2_gstacks stacks2_kmerfilter stacks2_populations stacks2_procrad stacks2_refmap stacks2_shortreads stacks2_sstacks stacks2_tsv2bam stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq			29267		stacks		To update	UseGalaxy.cz12 UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.no12 UseGalaxy.or12
stacks		stacks_assembleperead stacks_clonefilter stacks_cstacks stacks_denovomap stacks_genotypes stacks_populations stacks_procrad stacks_pstacks stacks_refmap stacks_rxstacks stacks_sstacks stacks_stats stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	Mapping Population genetics	Data handling	18086	stacks	stacks		To update	UseGalaxy.be11 UseGalaxy.cz13 UseGalaxy.eu13 UseGalaxy.fr12 UseGalaxy.no13 UseGalaxy.or13
srst2	0.2.0	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	Whole genome sequencing Public health and epidemiology Comparative genomics	Multilocus sequence typing	387	srst2	samtools		To update	UseGalaxy.cz1 UseGalaxy.eu1
sra_tools	3.1.1	fasterq_dump fastq_dump sam_dump	NCBI Sequence Read Archive toolkit utilities	DNA Genomics Sequencing	Data handling	1184364	sra-tools	sra-tools		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
squirrel	1.0.13	squirrel_phylo squirrel_qc	QC and Phylogenetic analysis of MPXV	Virology	Phylogenetic analysis Sequencing quality control	0	squirrel	squirrel		To update	UseGalaxy.eu2 UseGalaxy.or2
spyboat	0.1.2	spyboat	Wavelet analysis for 3d-image stacks			154		spyboat		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
spotyping	2.1	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	Microbiology Sequencing Sequence composition, complexity and repeats Genetic variation	Variant pattern analysis	1884	spotyping	spotyping		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
spapros	0.1.5	spapros_evaluation spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.		Primer and probe design Visualisation	3	spapros	spapros		Up-to-date	UseGalaxy.eu2
spaln	2.4.9	list_spaln_tables spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.			4911		python		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2 UseGalaxy.or2
spades	4.2.0	spades_biosyntheticspades spades_coronaspades spades_metaplasmidspades metaspades spades_metaviralspades spades_plasmidspades rnaspades spades_rnaviralspades spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	Sequence assembly	Genome assembly	304417	spades	spades		Up-to-date	UseGalaxy.be3 UseGalaxy.cz9 UseGalaxy.eu9 UseGalaxy.fr9 UseGalaxy.no3 UseGalaxy.or9
spacexr	2.2.1	spacexr_cside spacexr_rctd	Cell type identification and cell type-specific differential expression in spatial transcriptomics			0		r-spacexr		Up-to-date	UseGalaxy.eu2
sonneityping	20210201	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Whole genome sequencing Genotype and phenotype Genetic variation Metagenomics	Antimicrobial resistance prediction Variant calling Genotyping	1	sonneityping	sonneityping		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
socru	2.1.7	socru	Order and orientation of complete bacterial genomes			974		socru		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
snpfreqplot	1.0	snpfreqplot	A plotting app to visualise the SNPs across a region			6778		r-base		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
snpeff_sars_cov_2		snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	DNA polymorphism Genetic variation Nucleic acid sites, features and motifs	SNP detection	898538	snpeff			To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
snp_sites	2.5.1	snp_sites	Finds SNP sites from a multi-FASTA alignment file			11485		snp-sites		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
snp_dists	0.8.2	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment			15393		snp-dists		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
snippy		snippy_core snippy snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	Genomics Model organisms DNA polymorphism Phylogenetics	Phylogenetic tree visualisation Phylogenetic tree generation Variant calling	315480	snippy	snippy		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
snipit	1.6	snipit	Summarise snps relative to a reference sequence	Virology	Base position variability plotting	1039	snipit	snipit		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
sniffles	2.5.2	sniffles	Galaxy wrapper for sniffles	DNA structural variation Sequencing	Sequence analysis Structural variation detection	5140	sniffles	sniffles		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
snapatac2	2.6.4	snapatac2_clustering snapatac2_peaks_and_motif snapatac2_plotting snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis	Epigenomics Cell biology Chromosome conformation capture Mapping Sequencing	Essential dynamics Dimensionality reduction Gene expression profiling	2841	snapatac			To update	UseGalaxy.eu4 UseGalaxy.or4
snap	2013_11_29	snap snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	DNA DNA polymorphism Genetics	Gene prediction	3064	snap	snap		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
smudgeplot	0.2.5	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	Sequence assembly Genetic variation Mathematics	Sequence trimming Genotyping k-mer counting	1760	smudgeplots	smudgeplot		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
smallgenomeutilities	0.5.2	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	Genomics Population genetics Workflows Virology Sequencing	Read pre-processing Sequence alignment Genetic variation analysis	159	v-pipe	smallgenomeutilities		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
sleuth	0.30.2	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	RNA-Seq Gene expression Statistics and probability	Expression data visualisation Differential gene expression analysis Gene expression profiling Statistical calculation	181	sleuth	r-sleuth		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
slamdunk	0.4.3	alleyoop slamdunk	Slamdunk maps and quantifies SLAMseq reads			1528		slamdunk		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2 UseGalaxy.or2
sinto	0.10.1	sinto_barcode sinto_fragments	Sinto single-cell analysis tools	Bioinformatics Cell biology		633	sinto	sinto		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.or2
sina	1.7.2	sina	SINA reference based multiple sequence alignment	Sequencing RNA Nucleic acid structure analysis Taxonomy Sequence analysis Taxonomy	Sequence alignment analysis Multiple sequence alignment Taxonomic classification Structure-based sequence alignment	3894	sina	sina		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
simtext	0.0.2	abstracts_by_pmids pmids_to_pubtator_matrix pubmed_by_queries text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.			734		r-argparse		To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.or2
sickle	1.33.3	sickle	A windowed adaptive trimming tool for FASTQ files using quality	Data quality management	Sequence trimming	31761	sickle	sickle-trim		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
shovill	1.1.0	shovill	Faster de novo assembly pipeline based around Spades	Genomics Microbiology Sequence assembly	Genome assembly	134991	shovill	shovill		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
shorah_amplicon	1.1.3	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	Metagenomics Sequencing Genetics	Haplotype mapping Variant calling	0	shorah	shorah		To update
shasta	0.6.0	shasta	Fast de novo assembly of long read sequencing data			1810		shasta		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
sfold	2.2.0	sfold	Predict the probable RNA secondary structures through structure ensemble sampling			0				To update	UseGalaxy.eu1
seurat	5.0	seurat_create seurat_data seurat_integrate seurat_clustering seurat_preprocessing seurat_plot seurat_reduce_dimension	Seurat - R toolkit for single cell genomics	RNA-Seq Transcriptomics		2967	seurat	r-seurat		To update	UseGalaxy.eu7 UseGalaxy.fr6 UseGalaxy.or7
seqwish	0.7.5	seqwish	Alignment to variation graph inducer			271		seqwish		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
sequali	1.0.1	sequali	Fast sequencing data quality metrics for short and long reads	Data quality management Sequence analysis	Sequencing quality control Statistical calculation	0	sequali	sequali		Up-to-date	UseGalaxy.eu1
seqtk	1.5	seqtk_comp seqtk_cutN seqtk_dropse seqtk_fqchk seqtk_hety seqtk_listhet seqtk_mergefa seqtk_mergepe seqtk_mutfa seqtk_randbase seqtk_sample seqtk_seq seqtk_subseq seqtk_telo seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	Data management	Data handling Sequence file editing	437653	seqtk	seqtk		Up-to-date	UseGalaxy.be15 UseGalaxy.cz15 UseGalaxy.eu15 UseGalaxy.fr15 UseGalaxy.no14 UseGalaxy.or15
seqsero2	1.3.1	seqsero2	Salmonella serotype prediction from genome sequencing data	Whole genome sequencing Sequence assembly Genomics	Genome indexing Antimicrobial resistance prediction Genome alignment	13134	seqsero2	seqsero2		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
seqprep	1.3.2	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	Genomics Sequence assembly Sequencing Probes and primers	Nucleic acid design	2742	seqprep	seqprep		Up-to-date	UseGalaxy.eu1
seqkit	2.10.1	seqkit_fx2tab seqkit_grep seqkit_head seqkit_locate seqkit_sort seqkit_stats seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	Database management Sequence analysis	DNA transcription Sequence trimming DNA translation Sequence conversion	10086	seqkit	seqkit		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu6 UseGalaxy.fr5 UseGalaxy.or6
seqcomplexity	0.1.2	seqcomplexity	Sequence complexity for raw reads			202		seqcomplexity		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
seq2hla	2.3	seq2hla	Precision HLA typing and expression from RNAseq data	Transcriptomics Mapping	Read mapping Genetic variation analysis	433	seq2hla	seq2hla		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
semibin	2.1.0	semibin_bin semibin_concatenate_fasta semibin_generate_cannot_links semibin_generate_sequence_features semibin semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	Metagenomics Machine learning Microbial ecology Sequence assembly	Sequence assembly Read binning	1914	semibin	semibin		To update	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr1 UseGalaxy.or1
selenzy_wrapper	0.3.0	selenzy_wrapper	Performs enzyme selection from a reaction query.			0		selenzy_wrapper		Up-to-date
seacr	1.3	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.			13318		seacr		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
seaborn	0.13.2	seaborn seaborn_pairgrid	Seaborn is a Python data visualization library based on Matplotlib.			0		seaborn		To update
scpipe	1.0.0+galaxy2	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	Gene expression RNA-Seq Sequencing	Genome annotation Validation Alignment Visualisation	1419	scpipe	bioconductor-scpipe		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
scoary	1.6.16	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	Genotype and phenotype Model organisms GWAS study Functional genomics	Analysis	1120	scoary	scoary		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
scikit_bio	0.4.2	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics			2044		scikit-bio		Up-to-date	UseGalaxy.or1
schicexplorer	4	schicexplorer_schicadjustmatrix schicexplorer_schiccluster schicexplorer_schicclustercompartments schicexplorer_schicclusterminhash schicexplorer_schicclustersvl schicexplorer_schicconsensusmatrices schicexplorer_schiccorrectmatrices schicexplorer_schiccreatebulkmatrix schicexplorer_schicdemultiplex schicexplorer_schicinfo schicexplorer_schicmergematrixbins schicexplorer_schicmergetoscool schicexplorer_schicnormalize schicexplorer_schicplotclusterprofiles schicexplorer_schicplotconsensusmatrices schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.	Workflows DNA Chromosome conformation capture ChIP-seq Epigenetics	Validation Visualisation Standardisation and normalisation	1521	hicexplorer	schicexplorer		To update	UseGalaxy.be16 UseGalaxy.cz16 UseGalaxy.eu16 UseGalaxy.no16 UseGalaxy.or16
sceasy_convert	0.0.7	sceasy_convert	Converter between difference single-cell formats		Data handling	1998	sceasy	r-sceasy		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
scater	1.22.0	scater_create_qcmetric_ready_sce scater_filter scater_plot_dist_scatter scater_plot_pca scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	RNA-Seq Quality affairs Molecular genetics	Read pre-processing Sequencing quality control Sequence visualisation	2447	scater	bioconductor-scater		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5 UseGalaxy.or5
scanpy	1.10.2	scanpy_cluster_reduce_dimension scanpy_filter scanpy_inspect scanpy_normalize scanpy_plot scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	Gene expression Cell biology Genetics Single-cell sequencing	Differential gene expression analysis Principal component visualisation Expression profile clustering	123392	scanpy	scanpy		To update	UseGalaxy.be6 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.no6 UseGalaxy.or6
sbml2sbol	0.1.13	sbml2sbol	Convert SBML to SBOL format			0		sbml2sbol		To update
sarscov2summary	0.1	sarscov2summary	sarscov2summary custom script			393		sarscov2summary		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
sarscov2formatter	1.0	sarscov2formatter	sarscov2formatter custom script			574		sarscov2formatter		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
sansa	0.2.2	sansa_annotate	Sansa is a tool for structural variant annotation.			139		sansa		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
samblaster	0.1.26	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	DNA Sequencing Mapping	Split read mapping	0	samblaster	samblaster		Up-to-date
salsa	2.3	salsa	A tool to scaffold long read assemblies with Hi-C	Sequence assembly DNA binding sites Mapping	Genome assembly De-novo assembly Scaffolding	1934	SALSA	salsa2		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
ruvseq	1.26.0	ruvseq	Remove Unwanted Variation from RNA-Seq Data	Gene expression RNA-seq	Differential gene expression analysis	3737	ruvseq	bioconductor-ruvseq		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
rseqc	5.0.3	rseqc_FPKM_count rseqc_RNA_fragment_size rseqc_RPKM_saturation rseqc_bam2wig rseqc_bam_stat rseqc_clipping_profile rseqc_deletion_profile rseqc_geneBody_coverage rseqc_geneBody_coverage2 rseqc_infer_experiment rseqc_inner_distance rseqc_insertion_profile rseqc_junction_annotation rseqc_junction_saturation rseqc_mismatch_profile rseqc_read_GC rseqc_read_NVC rseqc_read_distribution rseqc_read_duplication rseqc_read_hexamer rseqc_read_quality rseqc_tin	an RNA-seq quality control package	Sequencing	Data handling	415667	rseqc	rseqc		To update	UseGalaxy.be22 UseGalaxy.cz22 UseGalaxy.eu22 UseGalaxy.fr22 UseGalaxy.no22 UseGalaxy.or22
rrparser	2.7.0	rrparser	Reaction Rules Parser			0		rrparser		To update
rptools	5.13.1	rptools_rpextractsink rptools_rpfba rptools_rpranker rptools_rpreport rptools_rpviz	Suite of tools that work on rpSBML format			0		rptools		To update
rpfba	5.12.3	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways			0		rptools		To update
rpbasicdesign	1.2.2	rpbasicdesign	Extracting enzyme IDs from rpSBML files			0		rpbasicdesign		To update
rp2paths	1.5.1	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0			0		rp2paths		To update
rp2biosensor	3.2.1	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output			0		rp2biosensor		To update
roary	3.13.0	roary	Roary the pangenome pipeline	DNA Genomics Mapping	Genome assembly	38357	roary	roary		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
rnaquast	2.3.0	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	Sequence assembly Transcriptomics RNA-Seq	De-novo assembly Transcriptome assembly Sequence assembly validation	2416	rnaQUAST	rnaquast		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
ribowaltz	1.2.0	ribowaltz_process ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	Computational biology		194	riboWaltz	ribowaltz		To update	UseGalaxy.cz2 UseGalaxy.eu2
rgrnastar	2.7.11b	rna_star rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	RNA-Seq Transcriptomics	Sequence alignment	1026347	star	star		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
rgcca	3.0.2	rgcca	multi-block analysis			131		rgccacmd		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
revoluzer	0.1.8	revoluzer_crex revoluzer_distmat	revoluzer wrappers	Molecular evolution Phylogeny	Structural variation detection	3046	revoluzer	revoluzer		Up-to-date	UseGalaxy.eu2
resize_coordinate_window	1.0.2	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.			303		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
reshape2	1.4.2	cast melt	Flexibly restructure and aggregate data using just the two functions melt and dcast			4179		r-reshape2		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
repmatch_gff3		repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.			722		matplotlib		To update	UseGalaxy.or1
repeatmodeler	2.0.5	repeatmodeler	RepeatModeler - Model repetitive DNA	Sequence composition, complexity and repeats Sequence composition, complexity and repeats	Repeat sequence detection	19323	repeatmodeler			To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
repeat_masker	4.1.5	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	Sequence analysis Sequence composition, complexity and repeats	Genome annotation	21398	repeatmasker	repeatmasker		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
red	2018.09.10	red	Red (REpeat Detector)	RNA Sequencing Data visualisation	RNA-Seq analysis Editing	1927	red	red		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
recentrifuge	1.16.1	recentrifuge	"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."	Metagenomics Microbial ecology Metagenomic sequencing	Taxonomic classification Expression analysis Cross-assembly	2477	Recentrifuge	recentrifuge		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
read_it_and_keep	0.2.2	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	Pathology Genomics	Filtering Genome alignment	3785	read_it_and_keep	read-it-and-keep		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
rcorrector	1.0.3+galaxy1	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	RNA RNA-Seq Sequencing	Sequencing error detection	779	rcorrector	rcorrector		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
raxml	8.2.12	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	Phylogenetics Sequence analysis	Sequence analysis Phylogenetic tree analysis	31039	raxml	raxml		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
raven	1.8.3	raven	Raven is a de novo genome assembler for long uncorrected reads.	Sequence assembly Whole genome sequencing Genomics	De-novo assembly Genome assembly Read pre-processing	23502	raven	raven-assembler		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
rasusa	2.0.0	rasusa	Randomly subsample sequencing reads to a specified coverage	Genomics Sequence analysis Sequence assembly Sequencing RNA-Seq	Sequence assembly validation Sequencing quality control	71	rasusa	rasusa		To update	UseGalaxy.eu1 UseGalaxy.fr1
rapidnj	2.3.2	rapidnj	Galaxy wrapper for the RapidNJ tool	Phylogeny	Phylogenetic tree generation	5100	rapidnj	rapidnj		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
ragtag	2.1.0	ragtag	Reference-guided scaffolding of draft genomes tool.	Sequence assembly	Genome assembly	6261	ragtag	ragtag		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
raceid	0.2.3	raceid_clustering raceid_filtnormconf raceid_inspectclusters raceid_inspecttrajectory raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis	Cell biology Molecular interactions, pathways and networks RNA-Seq Gene expression	Expression profile clustering Expression analysis Molecular dynamics	9983	RaceID	r-raceid		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr1 UseGalaxy.no5 UseGalaxy.or5
quicktree	2.5	quicktree	neighbour-joining phylogenetic inference	Phylogenetics	Phylogenetic inference (from molecular sequences)	65	quicktree	quicktree		Up-to-date	UseGalaxy.eu1
quickmerge	0.3	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	Structural variation Sequence assembly DNA polymorphism Whole genome sequencing Genotype and phenotype	Genome assembly Scaffolding De-novo assembly Genotyping	0	quickmerge	quickmerge		Up-to-date	UseGalaxy.no1
query_tabular	3.3.1	filter_tabular query_tabular sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output			168754		python		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr1 UseGalaxy.no3 UseGalaxy.or3
query_impc	0.9.0	query_impc	Contains a tool to query the IMPC database.			4		requests		To update	UseGalaxy.eu1
quast	5.3.0	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	Sequence assembly	Visualisation Sequence assembly validation	216176	quast	quast		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
qualimap	2.3	qualimap_bamqc qualimap_counts qualimap_multi_bamqc qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	Data quality management	Sequencing quality control	858426	qualimap	qualimap		Up-to-date	UseGalaxy.be4 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4 UseGalaxy.or4
qq_tools	0.1.0	qq_manhattan				16		r-qqman		To update	UseGalaxy.fr1
qiime_extract_viz	0.1.0	qiime_extract_viz	Extract vizualization from QIIME artifacts			104		unzip		To update	UseGalaxy.eu1 UseGalaxy.or1
qiime		qiime_align_seqs qiime_alpha_diversity qiime_alpha_rarefaction qiime_assign_taxonomy qiime_beta_diversity qiime_beta_diversity_through_plots qiime_compare_categories qiime_core_diversity qiime_count_seqs qiime_extract_barcodes qiime_filter_alignment qiime_filter_fasta qiime_filter_otus_from_otu_table qiime_filter_samples_from_otu_table qiime_filter_taxa_from_otu_table qiime_jackknifed_beta_diversity qiime_make_emperor qiime_make_otu_heatmap qiime_make_phylogeny qiime_multiple_join_paired_ends qiime_multiple_split_libraries_fastq qiime_pick_closed_reference_otus qiime_pick_open_reference_otus qiime_pick_otus qiime_pick_rep_set qiime_plot_taxa_summary qiime_split_libraries qiime_split_libraries_fastq qiime_summarize_taxa qiime_summarize_taxa_through_plots qiime_upgma_cluster qiime_validate_mapping_file	QIIME to perform microbial community analysis	Microbial ecology Phylogeny Metagenomics Metatranscriptomics	Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control	44433	qiime_core	qiime		To update	UseGalaxy.cz31 UseGalaxy.eu32 UseGalaxy.fr32 UseGalaxy.no31
qiime		qiime_collapse_samples qiime_make_otu_table	QIIME to perform microbial community analysis	Microbial ecology Phylogeny Metagenomics Metatranscriptomics	Demultiplexing Visualisation Taxonomic classification Phylogenetic analysis Sequencing quality control	2475	qiime_add_on	qiime		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2
qfilt	1.0.0+galaxy1	qfilt	Filter sequencing data			0		qfilt		To update
pysradb_search	1.4.2	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	Sequencing Gene transcripts Bioinformatics	Deposition Data retrieval	175	pysradb	pysradb		To update	UseGalaxy.cz1 UseGalaxy.eu1
pygenometracks	3.8	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	Model organisms Imaging Workflows	Visualisation Formatting	28461	pygenometracks	pygenometracks		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ega_download_client	5.0.2	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.			3123		pyega3		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
pycoqc	2.5.2	pycoqc	QC metrics for ONT Basecalling	Sequence analysis Data quality management Sequencing	Sequencing quality control Statistical calculation	27108	pycoqc	pycoqc		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
purge_dups	1.2.6	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	Sequence assembly	Genome assembly Read binning Scaffolding	22322	purge_dups	purge_dups		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
pureclip	1.0.4	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data			1559		pureclip		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
psiclass	1.0.3	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	Sequence assembly	Transcriptome assembly	26	psiclass	psiclass		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
proteinortho	6.3.6	proteinortho proteinortho_clustering proteinortho_grab_proteins proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	Comparative genomics	Sequence clustering Sequence analysis	4314	proteinortho	proteinortho		Up-to-date	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3
prot_scriber	0.1.6	prot_scriber	Protein annotation of short human readable descriptions			12		prot-scriber		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
prokka	1.14.6	prokka	Rapid annotation of prokaryotic genomes	Genomics Model organisms Virology	Gene prediction Coding region prediction Genome annotation	1132458	prokka	prokka		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
progressivemauve		progressivemauve xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner			5725		progressivemauve		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2 UseGalaxy.or2
prodigal	2.6.3	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	Genomics Sequence analysis	Genome annotation	4103	prodigal	prodigal		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
prinseq	@TOOL_VERSION+galaxy2	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	Transcriptomics Metagenomics Genomics	Read pre-processing Sequence trimming Sequence contamination filtering	24136	prinseq	prinseq		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
suite_pretext	0.0.7	pretext_graph pretext_map pretext_snapshot	Process genome contacts maps processing images.			8653		pretextgraph		To update	UseGalaxy.cz2 UseGalaxy.eu3 UseGalaxy.or2
presto	0.6.2	presto_alignsets presto_assemblepairs presto_buildconsensus presto_collapseseq presto_filterseq presto_maskprimers presto_pairseq presto_parseheaders presto_parselog presto_partition prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	Sequencing DNA Immunology	Nucleic acid sequence analysis	73477	presto	presto		To update	UseGalaxy.or11
ppanggolin	2.2.4	ppanggolin_all ppanggolin_msa ppanggolin_projection ppanggolin_rarefaction	Microbial Partitioned PanGenome	Metagenomics Gene and protein families Model organisms Public health and epidemiology Mapping	Rarefaction Essential dynamics Sequence assembly Genome annotation	0	ppanggolin	ppanggolin		Up-to-date	UseGalaxy.eu4 UseGalaxy.fr4
poretools	0.6.1a1	poretools_events poretools_extract poretools_hist poretools_nucdist poretools_occupancy poretools_qualdist poretools_qualpos poretools_squiggle poretools_stats poretools_tabular poretools_times poretools_winner poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	DNA Sequencing	Nucleic acid sequence analysis	73812	poretools	poretools		Up-to-date	UseGalaxy.cz13 UseGalaxy.eu13 UseGalaxy.no13 UseGalaxy.or13
porechop		porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads			483293		porechop		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
polypolish	0.6.1	polypolish	"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."	Sequence assembly Sequence composition, complexity and repeats Mapping	Genome assembly Read mapping Mapping assembly Sequencing error detection	1242	Polypolish	polypolish		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
plink	1.90b6.21	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	GWAS study	Genetic variation analysis	1865	plink	plink		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
plasmidfinder	2.1.6	plasmidfinder	"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"	Whole genome sequencing Sequence assembly Mapping Probes and primers	Genome assembly Scaffolding Multilocus sequence typing	32622	PlasmidFinder	plasmidfinder		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
plasflow	1.1.0	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	Metagenomics Sequence assembly Mobile genetic elements Machine learning	Sequence analysis	62172	plasflow	plasflow		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
plasclass	0.1.1	plasclass	PlasClass is a tool to classify sequences of plasmid or chromosomal origin	Metagenomics Sequence assembly DNA Metagenomic sequencing	Sequence classification Sequence assembly k-mer counting	0	PlasClass	plasclass		Up-to-date
pizzly	0.37.3.1	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.			1948		pizzly		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
pipelign	0.2	pipelign	Multipe sequence alignment			10918		pipelign		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
pimento	1.0.2	pimento_are_there_primers pimento_auto pimento_choose_primer_cutoff pimento_find_cutoffs pimento_gen_bcv pimento_std	A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants.			0		mi-pimento		Up-to-date	UseGalaxy.eu6
pilon	1.20.1	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	Assembly	Sequence assembly Analysis Read alignment	23352	pilon	pilon		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
picrust2	2.5.3	picrust2_add_descriptions picrust2_hsp picrust2_metagenome_pipeline picrust2_pathway_pipeline picrust2_pipeline picrust2_place_seqs picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	Metagenomics Microbiology Phylogenetics Metagenomic sequencing	Phylogenetic reconstruction Expression analysis Rarefaction Pathway analysis	5428	picrust2	picrust2		To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.or7
picrust	1.1.1	picrust_categorize picrust_compare_biom picrust_format_tree_and_trait_table picrust_metagenome_contributions picrust_normalize_by_copy_number picrust_predict_metagenomes	PICRUSt wrappers	Metagenomics Microbial ecology Functional, regulatory and non-coding RNA Metagenomic sequencing	Phylogenetic reconstruction Expression analysis Genome annotation DNA barcoding	3887	picrust	picrust		To update	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr6 UseGalaxy.no5 UseGalaxy.or6
pick_value	0.2.0	pick_value	Compose a text parameter value using text, integer and float values			9960				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
picard	3.1.1	picard_AddCommentsToBam picard_AddOrReplaceReadGroups picard_BedToIntervalList picard_CleanSam picard_CASM picard_CollectBaseDistributionByCycle picard_CollectGcBiasMetrics picard_CollectHsMetrics picard_CollectInsertSizeMetrics picard_CollectRnaSeqMetrics picard_artifact_metrics picard_CollectWgsMetrics picard_DownsampleSam picard_EstimateLibraryComplexity picard_FastqToSam picard_FilterSamReads picard_FixMateInformation picard_MarkDuplicates picard_MarkDuplicatesWithMateCigar picard_MeanQualityByCycle picard_MergeBamAlignment picard_MergeSamFiles picard_NormalizeFasta picard_QualityScoreDistribution picard_ReorderSam picard_ReplaceSamHeader picard_RevertOriginalBaseQualitiesAndAddMateCigar picard_RevertSam picard_SamToFastq picard_SortSam picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	Sequencing	Formatting	1143229	picard_samtofastq	picard		To update	UseGalaxy.be31 UseGalaxy.cz31 UseGalaxy.eu31 UseGalaxy.fr31 UseGalaxy.no31 UseGalaxy.or31
phyml	3.3.20220408	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	Phylogenetics Bioinformatics Phylogenetics	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	3095	phyml	phyml		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
phyloseq	1.50.0	phyloseq_add_rank_names phyloseq_from_biom phyloseq_from_dada2 phyloseq_plot_bar phyloseq_plot_ordination phyloseq_plot_richness phyloseq_tax_glom	Handling and analysis of high-throughput microbiome census data	Microbiology Sequence analysis Metagenomics	Deposition Analysis Visualisation	2248	phyloseq	bioconductor-phyloseq		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu7 UseGalaxy.fr6 UseGalaxy.no3 UseGalaxy.or1
pharokka	1.3.2	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	Metagenomics Sequence sites, features and motifs Workflows Functional, regulatory and non-coding RNA	Genome annotation Antimicrobial resistance prediction tRNA gene prediction Formatting Sequence assembly	11358	pharokka	pharokka		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
pgxrpi	1.2.0	pgx_freqplot pgx_loader	pgxLoader and pgxFreqplot functions from pgxRpi			0		bioconductor-pgxrpi		Up-to-date
pear	0.9.6	iuc_pear	PEAR evaluates all possible paired-end read overlaps	Sequence assembly	Sequence merging	37315	pear	pear		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
peakzilla	1.0	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.			40		python		To update	UseGalaxy.eu1
pe_histogram	1.0.2	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.			17759		openjdk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
pdfimages	25.07.0	pdfimages	PDF image extractor.			0		poppler		To update	UseGalaxy.eu1
pcdl	3.0.1+galaxy0	pcdl_get_anndata pcdl_get_cell_attribute pcdl_get_cell_attribute_list pcdl_get_cell_df pcdl_get_celltype_list pcdl_get_conc_attribute pcdl_get_conc_df pcdl_get_substrate_list pcdl_get_unit_dict pcdl_get_version pcdl_make_cell_vtk pcdl_make_conc_vtk pcdl_make_gif pcdl_make_graph_gml pcdl_make_movie pcdl_plot_contour pcdl_plot_scatter pcdl_plot_timeseries	pcdl PhysiCell Data Loader.			0				To update	UseGalaxy.eu18
bam2fastx	3.5.0	bam2fastx	Convert PacBio Bam File to fasta or fastq file			403		pbtk		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
pbmm2	1.17.0	pbmm2	A minimap2 SMRT wrapper for PacBio data.	Mapping	Pairwise sequence alignment Sorting	122	pbmm2	pbmm2		Up-to-date	UseGalaxy.eu1
pbgcpp	2.0.2	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	Mapping	Variant calling	0	genomicconsensus	pbgcpp		Up-to-date
pathview	1.34.0	pathview	Pathview is a tool set for pathway based data integration and visualization.	Molecular interactions, pathways and networks Systems biology Data visualisation	Pathway or network analysis Pathway or network visualisation	16877	pathview	bioconductor-pathview		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
parse_mito_blast	1.0.2	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.			1057		parse_mito_blast		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
pangolin	4.3	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	Virology	Tree-based sequence alignment Variant classification	19682	pangolin_cov-lineages	pangolin		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
panaroo	1.5.2	panaroo	A Bacterial Pangenome Analysis Pipeline	Workflows Sequence assembly Gene and protein families Plant biology Sequencing	De-novo assembly Genome assembly Clustering	129	panaroo	panaroo		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
pairtools	1.1.3	pairtools_dedup pairtools_parse pairtools_sort pairtools_split pairtools_stats	Flexible tools for Hi-C data processing			406		pairtools		Up-to-date	UseGalaxy.eu5 UseGalaxy.or5
pacu	0.0.5	pacu_map pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	Phylogenetics Sequence analysis	Clustering	55	pacu	pacu_snp		To update	UseGalaxy.eu2
packaged_annotation_loader	0.1	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection			0		python		To update
orthofinder	2.5.5	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	Phylogenetics Phylogenomics Bioinformatics Comparative genomics Sequence analysis	Genome comparison Phylogenetic tree generation (from molecular sequences) Phylogenetic tree analysis Genome alignment	3759	OrthoFinder	orthofinder		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
orfipy	0.0.4	orfipy	Galaxy wrapper for ORFIPY	Computer science RNA-Seq Transcriptomics Small molecules	Coding region prediction Database search Transcriptome assembly De-novo assembly	3285	orfipy	orfipy		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
optitype	1.3.5	optitype	Precision HLA typing from NGS data			627		optitype		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
optdoe	v2.0.2	optdoe	Optimal Design Of Experiment			0		doebase		To update
openalex_explorer	0.1.0+galaxy0	openalex_explorer	Fetch citing papers from OpenAlex using DOI, ID and title			0		python		To update	UseGalaxy.eu1
onto_toolkit	1.45	onto_tk_get_ancestor_terms onto_tk_get_child_terms onto_tk_get_descendent_terms onto_tk_get_parent_terms onto_tk_get_parent_terms_by_relationship_type onto_tk_get_relationship_id_vs_relationship_def onto_tk_get_relationship_id_vs_relationship_name onto_tk_get_relationship_id_vs_relationship_namespace onto_tk_get_relationship_types onto_tk_get_root_terms onto_tk_get_subontology_from onto_tk_term_id_vs_term_def onto_tk_term_id_vs_term_name onto_tk_get_term_synonyms onto_tk_get_terms onto_tk_get_terms_by_relationship_type onto_tk_obo2owl onto_tk_obo2rdf onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.			665		perl-onto-perl		Up-to-date	UseGalaxy.cz17 UseGalaxy.eu17 UseGalaxy.no17
ont_fast5_api	3.1.3	ont_fast5_api_compress_fast5 ont_fast5_api_fast5_subset ont_fast5_api_multi_to_single_fast5 ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.			3090		ont-fast5-api		To update	UseGalaxy.be4 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no4
omark	0.3.1	omark	Proteome quality assessment software	Proteomics Sequence analysis Statistics and probability	Sequence assembly validation Differential protein expression profiling	741	omark			To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
odgi	0.3	odgi_build odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.			29		odgi		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2
ococo	0.1.2.6	ococo	Variant detection of SNVs			3508		ococo		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
obitools	1.2.13	obi_illumina_pairend obi_ngsfilter obi_annotate obi_clean obi_convert obi_grep obi_sort obi_stat obi_tab obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	Sequence analysis DNA Sequencing	Sequence analysis Sequence analysis	46515	obitools	obitools		Up-to-date	UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr10 UseGalaxy.no10 UseGalaxy.or10
nugen_nudup	2.3.3	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	Sequencing Genomics	Duplication detection Sequence analysis	0	nudup	nudup		Up-to-date
novoplasty	4.3.1	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.			12003		novoplasty		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
nonpareil	3.5.5	nonpareil	Estimate average coverage in metagenomic datasets		Operation	305	nonpareil	nonpareil		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ngsutils		ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	Genomics Transcriptomics	Read pre-processing Sequencing quality control Variant calling Formatting Sequence contamination filtering	66759	ngsutils	ngsutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ngmlr	0.2.7	ngmlr	CoNvex Gap-cost alignMents for Long Reads	Sequencing Mapping DNA structural variation	DNA mapping Sequence alignment Genetic variation analysis	1406	ngmlr	ngmlr		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
nextclade	2.7.0	nextalign nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	Genomics Sequence analysis Cladistics	Methylation analysis Variant calling	18621	nextclade	nextalign		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or1
newick_utils	1.6+galaxy1	newick_display	Perform operations on Newick trees	Phylogeny Genomics Computer science	Phylogenetic tree generation Phylogenetic tree analysis Phylogenetic tree reconstruction	64737	newick_utilities	newick_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
necat	0.0.1_update20200803	necat	Error correction and de-novo assembly for ONT Nanopore reads	Sequence assembly	De-novo assembly	975	necat	necat		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
ncbi_fcs_gx	0.5.5	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	Sequence analysis Sequence assembly	Sequence assembly validation Sequence trimming Sequence contamination filtering	6770	ncbi_fcs	ncbi-fcs-gx		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
ncbi_entrez_eutils	1.70	ncbi_eutils_ecitmatch ncbi_eutils_efetch ncbi_eutils_einfo ncbi_eutils_elink ncbi_eutils_epost ncbi_eutils_esearch ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases			3235		python		To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.no7
ncbi_entrez_direct	22.4	ncbi_entrez_direct_efetch ncbi_entrez_direct_einfo ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases			3		entrez-direct		To update
ncbi_datasets	18.5.1	datasets_download_gene datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	Biological databases	Data handling Sequence database search Data retrieval	20804	ncbi_datasets	ncbi-datasets-cli		To update	UseGalaxy.be1 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
ncbi_acc_download	0.2.8	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API			34900		ncbi-acc-download		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
nanopolishcomp	0.6.11	nanopolishcomp_eventaligncollapse nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	Sequence analysis Sequencing Genetic variation	Methylation analysis Collapsing methods	1120	nanopolishcomp	nanopolishcomp		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2
nanoplot	1.46.1	nanoplot	Plotting tool for long read sequencing data and alignments	Genomics	Scatter plot plotting Box-Whisker plot plotting	193928	nanoplot	nanoplot		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
nanocompore	1.0.0rc3.post2	nanocompore_db nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Functional, regulatory and non-coding RNA RNA-Seq Gene transcripts Transcriptomics Transcription factors and regulatory sites	Post-translation modification site prediction PolyA signal detection Genotyping k-mer counting	1150	Nanocompore	nanocompore		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2 UseGalaxy.or1
nanocomp	1.25.3	nanocomp	Compare multiple runs of long read sequencing data and alignments	Nucleic acids Bioinformatics	Box-Whisker plot plotting Visualisation Multiple sample visualisation	0	nanocomp	nanocomp		To update	UseGalaxy.eu1
naltorfs	0.1.2	bicodon_counts_from_fasta codon_freq_from_bicodons find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)			228		naltorfs		Up-to-date	UseGalaxy.or3
mzmine_batch	3.9.0	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	Proteomics Metabolomics Proteomics experiment Small molecules	Natural product identification Standardisation and normalisation Peptide database search Deisotoping Clustering Filtering Chromatographic alignment Peak detection Peptide identification Chromatogram visualisation Mass spectrum visualisation Structure visualisation Plotting Heat map generation	11	mzmine	mzmine		To update	UseGalaxy.eu1
mykrobe	0.10.0	mykrobe_predict	Antibiotic resistance predictions	Whole genome sequencing Genotype and phenotype Probes and primers Genetic variation Metagenomics	Antimicrobial resistance prediction Variant calling Genotyping Sequence trimming	0	Mykrobe	mykrobe		To update
muon	0.1.6	cluster_analyze_embed_muon mudata_import_export plot_muon preprocess_muon	muon is a Python framework for multimodal omics analysis	Cell biology Single-cell sequencing Gene expression Epigenetics Multiomics		0	muon	muon		To update	UseGalaxy.eu4
mummer4	4.0.0	mummer_delta_filter mummer_dnadiff mummer_mummer mummer_mummerplot mummer_nucmer mummer_show_coords	Mummer4 Tools	Sequence analysis Human genetics	Multiple sequence alignment	65097	mummer4	mummer4		To update	UseGalaxy.be6 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.no6 UseGalaxy.or6
multiqc	1.27	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	Sequencing Bioinformatics Sequence analysis Genomics	Validation Sequencing quality control	498453	multiqc	multiqc		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
multigsea	1.12.0	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	Metabolomics Molecular interactions, pathways and networks Proteomics Transcriptomics Small molecules	Gene-set enrichment analysis Aggregation Pathway analysis	159	multiGSEA	bioconductor-multigsea		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
multigps	0.74.0	multigps	Analyzes collections of multi-condition ChIP-seq data.			886		fonts-conda-ecosystem		To update	UseGalaxy.or1
msaboot	0.1.2	msaboot	A multiple sequences alignment bootstrapping tool.			2169		msaboot		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
mothur	1.0	mothur_align_check mothur_align_seqs mothur_amova mothur_anosim mothur_bin_seqs mothur_biom_info mothur_chimera_bellerophon mothur_chimera_ccode mothur_chimera_check mothur_chimera_perseus mothur_chimera_pintail mothur_chimera_slayer mothur_chimera_uchime mothur_chimera_vsearch mothur_chop_seqs mothur_classify_otu mothur_classify_seqs mothur_classify_tree mothur_clearcut mothur_cluster_classic mothur_cluster_fragments mothur_cluster_split mothur_cluster mothur_collect_shared mothur_collect_single mothur_consensus_seqs mothur_cooccurrence mothur_corr_axes mothur_count_groups mothur_count_seqs mothur_create_database mothur_degap_seqs mothur_deunique_seqs mothur_deunique_tree mothur_dist_seqs mothur_dist_shared mothur_fastq_info mothur_filter_seqs mothur_filter_shared mothur_get_communitytype mothur_get_coremicrobiome mothur_get_dists mothur_get_group mothur_get_groups mothur_get_label mothur_get_lineage mothur_get_mimarkspackage mothur_get_otulabels mothur_get_otulist mothur_get_oturep mothur_get_otus mothur_get_rabund mothur_get_relabund mothur_get_sabund mothur_get_seqs mothur_get_sharedseqs mothur_heatmap_bin mothur_heatmap_sim mothur_homova mothur_indicator mothur_lefse mothur_libshuff mothur_list_otulabels mothur_list_seqs mothur_make_biom mothur_make_contigs mothur_make_design mothur_make_fastq mothur_make_group mothur_make_lefse mothur_make_lookup mothur_make_shared mothur_make_sra mothur_mantel mothur_merge_count mothur_merge_files mothur_merge_groups mothur_merge_sfffiles mothur_merge_taxsummary mothur_metastats mothur_mimarks_attributes mothur_nmds mothur_normalize_shared mothur_otu_association mothur_otu_hierarchy mothur_pairwise_seqs mothur_parse_list mothur_parsimony mothur_pca mothur_pcoa mothur_pcr_seqs mothur_phylo_diversity mothur_phylotype mothur_pre_cluster mothur_primer_design mothur_rarefaction_shared mothur_rarefaction_single mothur_remove_dists mothur_remove_groups mothur_remove_lineage mothur_remove_otulabels mothur_remove_otus mothur_remove_rare mothur_remove_seqs mothur_rename_seqs mothur_reverse_seqs mothur_screen_seqs mothur_sens_spec mothur_seq_error mothur_sffinfo mothur_shhh_flows mothur_shhh_seqs mothur_sort_seqs mothur_split_abund mothur_split_groups mothur_sub_sample mothur_summary_qual mothur_summary_seqs mothur_summary_shared mothur_summary_single mothur_summary_tax mothur_taxonomy_to_krona mothur_tree_shared mothur_trim_flows mothur_trim_seqs mothur_unifrac_unweighted mothur_unifrac_weighted mothur_unique_seqs mothur_venn	Mothur wrappers	Microbial ecology Taxonomy Sequence analysis Phylogeny	DNA barcoding Sequencing quality control Sequence clustering Taxonomic classification Visualisation Sequence read processing Phylogenetic analysis	1262671	mothur	mothur		To update	UseGalaxy.be126 UseGalaxy.cz129 UseGalaxy.eu129 UseGalaxy.fr129 UseGalaxy.no129 UseGalaxy.or129
mosdepth	0.3.11	mosdepth	fast and flexible BAM/CRAM depth calculation			21679		mosdepth		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
moabs	1.3.4.6	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.			349		moabs		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
mmuphin	1.16.0	mmuphin	MMUPHin is an R package implementing meta-analysis methods for microbial community profiles			0	mmuphin	bioconductor-mmuphin		Up-to-date	UseGalaxy.eu1
mmseqs2	17-b804f	mmseqs2_easy_linclust_clustering mmseqs2_taxonomy_assignment	MMseqs2 is an ultra fast and sensitive sequence search and clustering suite	Metagenomics Sequence analysis Proteins Nucleic acids Gene and protein families Taxonomy	Sequence similarity search Sequence alignment Sequence clustering Taxonomic classification	0	MMseqs2	mmseqs2		To update	UseGalaxy.eu2 UseGalaxy.fr2
mlst	2.22.0	mlst mlst_list	Scan contig files against PubMLST typing schemes	Immunoproteins and antigens	Multilocus sequence typing	42341	mlst	mlst		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
mitos	1.1.7	mitos mitos2	de-novo annotation of metazoan mitochondrial genomes	Zoology Whole genome sequencing	Genome annotation	322857	mitos	mitos		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no1 UseGalaxy.or1
mitobim	1.9.1	mitobim	assemble mitochondrial genomes			1687		mitobim		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
mirnature	1.1	mirnature	Computational detection of canonical microRNAs			22		mirnature		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
mirmachine	0.3.0.1	mirmachine	Tool to detect miRNA in genome sequences			7		mirmachine		Up-to-date	UseGalaxy.eu1
miniprot	0.18	miniprot miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	Sequence sites, features and motifs Sequence analysis	Sequence alignment Protein sequence analysis	5362	miniprot	miniprot		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
minimap2	2.28	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	Mapping	Pairwise sequence alignment	555047	minimap2	minimap2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
miniasm	0.3_r179	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	Genomics Sequence assembly	De-novo assembly	24708	miniasm	miniasm		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
minia	3.2.6	minia	Short-read assembler based on a de Bruijn graph	Sequence assembly	Genome assembly	7460	minia	minia		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
migmap	1.0.3	migmap	mapper for full-length T- and B-cell repertoire sequencing	Immunoproteins, genes and antigens Sequence analysis	Sequence analysis Read mapping	2684	MiGMAP	migmap		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
microsatbed	1.3.3	microsatbed	Select microsatellites for a bed file			1617		python		To update	UseGalaxy.eu1 UseGalaxy.or1
micro_decon	1.0.2	micro_decon	An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing			0				To update	UseGalaxy.eu1
mg_toolkit	0.10.4	mg_toolkit_bulk_download mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Metagenomics	Data retrieval	13	mg-toolkit	mg-toolkit		Up-to-date	UseGalaxy.eu2
metawrapmg_binning	1.3.0	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	Whole genome sequencing Metagenomic sequencing Metagenomics	Read binning Sequence assembly Genome annotation Sequence trimming Demultiplexing	922	metawrap	metawrap-mg		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
metasbt	0.1.5	metasbt_index metasbt_profile	Microbial genomes characterization with Sequence Bloom Trees			0		sed		To update	UseGalaxy.eu2
metaphlan	4.1.1	customize_metaphlan_database extract_metaphlan_database merge_metaphlan_tables metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	Metagenomics Phylogenomics	Taxonomic classification Taxonomic classification	37088	metaphlan	metaphlan		To update	UseGalaxy.be1 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4 UseGalaxy.or2
metagenomeseq_normalization	1.16.0-0.0.1	metagenomeseq_normalizaton	metagenomeSeq Normalization	Metagenomics Sequencing	Sequence visualisation Statistical calculation	1288	metagenomeseq	bioconductor-metagenomeseq		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
metaeuk	7.bba0d80	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand.	Metagenomics Gene and protein families	Homology-based gene prediction	496	MetaEuk	metaeuk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
metabuli	1.0.5	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	Taxonomy	Taxonomic classification	0	metabuli	metabuli		To update	UseGalaxy.eu1
metabat2	2.17	metabat2_jgi_summarize_bam_contig_depths metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	Metagenomics Sequence assembly Metagenomic sequencing	Read binning Sequence assembly Genome annotation	12254	MetaBAT_2	metabat2		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or1
meryl	1.3	meryl_arithmetic_kmers meryl_count_kmers meryl_filter_kmers meryl_groups_kmers meryl_histogram_kmers meryl_print meryl_trio_mode	Meryl a k-mer counter.	Whole genome sequencing Genomics Sequence analysis Sequencing	k-mer counting	211	meryl	merqury		Up-to-date	UseGalaxy.eu7 UseGalaxy.or7
merquryfk	1.1.1	merquryfk_asmplot merquryfk_cnplot merquryfk_hapmaker merquryfk_happlot merquryfk_merquryfk	FastK based version of Merqury			0		merquryfk		To update
merqury	1.3	merqury merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	Sequence assembly Whole genome sequencing Plant biology	Genome assembly k-mer counting Scaffolding Phasing De-novo assembly	6560	merqury	merqury		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
merlin	1.1.2	merlin	Pedigree Analysis package	GWAS study Mapping	Haplotype mapping Genetic mapping	0	merlin	merlin		Up-to-date
meningotype	0.8.5	meningotype	Assign sequence type to N. meningitidis genome assemblies	Microbiology Genotype and phenotype	Genotyping Multilocus sequence typing	0	meningotype	meningotype		Up-to-date
meme_chip	4.11.2	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.			15133		graphicsmagick		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
meme	5.5.8	meme_dreme meme_fimo meme_meme meme_psp_gen meme_streme	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	Sequence sites, features and motifs ChIP-seq RNA immunoprecipitation Epigenetics Small molecules	Sequence motif discovery Sequence motif recognition Sequence motif comparison Transcriptional regulatory element prediction	50605	streme	meme		Up-to-date	UseGalaxy.be3 UseGalaxy.cz4 UseGalaxy.eu5 UseGalaxy.no4 UseGalaxy.or3
megan	6.21.7	megan_blast2lca megan_blast2rma megan_daa2info megan_daa2rma megan_daa_meganizer megan_read_extractor megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	Sequence analysis	Sequence analysis Taxonomic classification	4619	megan	megan		To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.or1
megahit_contig2fastg	1.1.3	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	Metagenomics Sequencing Ecology Sequence assembly	Genome assembly	927	megahit	megahit		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
megahit	1.2.9	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	Metagenomics Sequencing Ecology Sequence assembly	Genome assembly	44056	megahit	megahit		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
medaka	1.7.2	medaka_consensus medaka_consensus_pipeline medaka_snp medaka_variant	Sequence correction provided by ONT Research	Sequence assembly Machine learning	Base-calling Variant calling Sequence assembly	199240	medaka	medaka		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
mcl	22.282	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	Molecular interactions, pathways and networks	Clustering Network analysis Gene regulatory network analysis	153	mcl	mcl		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
maxbin2		maxbin2	clusters metagenomic contigs into bins	Metagenomics Sequence assembly Microbiology	Sequence assembly	7691	maxbin	maxbin2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
masigpro	1.49.3	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	Gene expression Molecular genetics Microarray experiment RNA-Seq	Regression analysis	1186	masigpro	coreutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
mashmap	3.1.3	mashmap	Fast local alignment boundaries			2291		mashmap		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
mash	2.3	mash_screen mash_sketch	Fast genome and metagenome distance estimation using MinHash	Genomics Metagenomics Statistics and probability Sequence analysis DNA mutation	Sequence distance matrix generation	12505	mash	mash		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
mapseq	2.1.1b	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	Functional, regulatory and non-coding RNA Sequence analysis Sequence sites, features and motifs	k-mer counting	9229	mapseq	perl		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
maplot	1.0.0	maplot	Generate MA plots for visualizing data distributions using Plotly or Matplotlib.			0		plotly		To update
map_param_value	0.2.0	map_param_value	Map a parameter value to another value			7042				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
map_damage	2.2.3	map_damage	Tracks and quantifies specific ancient DNA damage patterns for authentication.	DNA Sequencing	Sequencing quality control Statistical calculation	0	mapdamage	mapdamage2		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
malt_run	0.5.3	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.			25		malt		To update	UseGalaxy.cz1 UseGalaxy.eu1
maker	2.31.11	maker maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genomics DNA Sequence analysis	Genome annotation	21746	maker	maker		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
mageck	0.5.9.2	mageck_count mageck_gsea mageck_mle mageck_pathway mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetics Genetic variation Genomics	Genetic variation analysis	28661	mageck	mageck		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or5
maf_stats	1.0.2+galaxy0	maf_stats1	MAF Coverage statistics			2501				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
macs2	2.2.9.1	macs2_bdgbroadcall macs2_bdgcmp macs2_bdgdiff macs2_bdgpeakcall macs2_callpeak macs2_filterdup macs2_predictd macs2_randsample macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	ChIP-seq Molecular interactions, pathways and networks Transcription factors and regulatory sites	Peak calling Enrichment analysis Gene regulatory network analysis	365381	macs	macs2		Up-to-date	UseGalaxy.be9 UseGalaxy.cz9 UseGalaxy.eu9 UseGalaxy.fr9 UseGalaxy.no9 UseGalaxy.or9
maaslin2	1.18.0	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	Metagenomics Statistics and probability	Filtering Statistical calculation Standardisation and normalisation Visualisation	3109	maaslin2	bioconductor-maaslin2		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
m6anet	2.1.0	m6anet	m6anet to detect m6A RNA modifications from nanopore data	RNA-Seq Transcriptomics RNA Machine learning	Quantification Imputation Gene expression profiling	44	m6Anet	m6anet		Up-to-date	UseGalaxy.eu1 UseGalaxy.no1
lumpy_sv	0.3.1	lumpy_prep lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery			2121		lumpy-sv		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2
lorikeet_spoligotype	20	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Genotype and phenotype	Sequence analysis Genotyping	903	lorikeet	lorikeet		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
lofreq	2.1.5	lofreq_alnqual lofreq_call lofreq_filter lofreq_indelqual lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.			4855707		lofreq		Up-to-date	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr4 UseGalaxy.no5 UseGalaxy.or5
links	2.0.1	links	Scaffold genome assemblies with long reads.	Sequence assembly Mapping Sequencing	Scaffolding Genome assembly Read mapping Read pre-processing Sequence trimming	1225	links	links		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
lineagespot	1.6.0	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	Metagenomics Gene transcripts Evolutionary biology Sequencing Genetic variation	Variant calling	39	lineagespot	r-base		To update	UseGalaxy.cz1 UseGalaxy.eu1
limma_voom	3.58.1	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	Molecular biology Genetics	RNA-Seq analysis	92039	limma	bioconductor-limma		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
length_and_gc_content	0.1.2	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file			7657		r-optparse		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
legsta	0.5.1	legsta	Performs in silico Legionella pneumophila sequence based typing.	Public health and epidemiology	Sequence analysis	103	legsta	legsta		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
lcrgenie	1.0.2	lcrgenie	Ligase Chain Reaction Genie			0		lcr_genie		To update
lastz	1.04.22	lastz_wrapper_2 lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	Genomics	Sequence alignment Read mapping	325060	lastz	lastz		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
last	1205	last_al last_db last_split last_train last_maf_convert	LAST finds similar regions between sequences.	Genomics Comparative genomics	Sequence alignment	383	last	last		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5
krocus	1.0.1	krocus	Predict MLST directly from uncorrected long reads	Public health and epidemiology	Multilocus sequence typing k-mer counting	0	krocus	krocus		To update	UseGalaxy.eu1
krakentools	1.2.1	krakentools_alpha_diversity krakentools_beta_diversity krakentools_combine_kreports krakentools_extract_kraken_reads krakentools_kreport2krona krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	Taxonomy Metagenomics	Visualisation Aggregation	139895	krakentools	krakentools		Up-to-date	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.no1 UseGalaxy.or6
kraken_taxonomy_report	0.0.3	kraken_taxonomy_report	Kraken taxonomy report	Metagenomics Taxonomy	Visualisation Classification	11014	Kraken-Taxonomy-Report	biopython		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
kraken_biom	1.2.0	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)	Metagenomics Taxonomy	Genome annotation Taxonomic classification	4437	kraken-biom	kraken-biom		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
kofamscan	1.3.0	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	Genomics Structure analysis	Sequence analysis Gene functional annotation	1646	kofamscan	kofamscan		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
kmer2stats	1.0.1	kmer2stats	A tool for creating data files for statistics based on kmers			0		kmer2stats		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
kma	1.5.1	kma_map	Map with KMA			1		kma		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
kleborate	2.3.2	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	Public health and epidemiology Metagenomics Population genomics Sequence assembly Whole genome sequencing	Multilocus sequence typing Genome assembly Virulence prediction	650	kleborate	kleborate		To update	UseGalaxy.cz1 UseGalaxy.eu1
king	2.2.7	king	Kinship-based INference for Gwas			8		king		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
khmer	3.0.0a3	khmer_abundance_distribution_single khmer_abundance_distribution khmer_count_median khmer_partition khmer_extract_partitions khmer_filter_abundance khmer_filter_below_abundance_cutoff khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	Sequence assembly	Standardisation and normalisation De-novo assembly	5499	khmer	khmer		Up-to-date	UseGalaxy.be8 UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.no8 UseGalaxy.or8
kc_align	1.0.2	kc-align	Kc-Align custom tool	Mapping	Multiple sequence alignment	8688	kc-align	kcalign		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
kallisto	0.48.0	kallisto_pseudo kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	Transcriptomics RNA-Seq Gene expression	Gene expression profiling	124410	kallisto	kallisto		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
kaiju	1.10.1	kaiju_addtaxonnames kaiju_mergeoutputs kaiju_kaiju kaiju_kaiju2krona kaiju_kaiju2table	taxonomic classification of high-throughput sequencing reads	Metagenomics	Taxonomic classification	0	kaiju	kaiju		Up-to-date	UseGalaxy.eu5
jvarkit	20201223	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics			21926		jvarkit-wgscoverageplotter		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
jq	1.0	jq	JQ is a lightweight and flexible command-line JSON processor			3059		jq		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
join_files_by_id	1.0	join_files_by_id	This tool will join datasets according to a column with identifier			0		r-data.table		To update
jellyfish		jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Sequence analysis Genomics	k-mer counting	4689	Jellyfish	kmer-jellyfish		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
jcvi_gff_stats	0.8.4	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)			7543		jcvi		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
jbrowse	1.16.11	jbrowse_to_standalone jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	Genomics	Genome visualisation	64507	jbrowse	jbrowse		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
jasminesv	1.0.11	jasminesv	Merge structural variants across samples			94		jasminesv		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
iwtomics	1.0.0	iwtomics_loadandplot iwtomics_plotwithscale iwtomics_testandplot	Interval-Wise Testing for Omics Data	Statistics and probability	Differential gene expression analysis Differentially-methylated region identification Peak calling Genome annotation Comparison	1396	iwtomics	bioconductor-iwtomics		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.no3 UseGalaxy.or3
ivar	1.4.4	ivar_consensus ivar_filtervariants ivar_removereads ivar_trim ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing	Virology	Primer removal	1508647	andersen-lab_ivar	ivar		Up-to-date	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or5
isoformswitchanalyzer	1.20.0	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	Computational biology Gene transcripts	Sequence comparison Sequence analysis	4323	IsoformSwitchAnalyzeR	bioconductor-isoformswitchanalyzer		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
ISEScan	1.7.3	isescan	"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."	Genomics DNA structural variation Sequence analysis Genetic variation	Structural variation detection	69744	ISEScan	isescan		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
irma	1.2.0	irma	Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses.		Mapping assembly	7548	irma-virus	irma		Up-to-date	UseGalaxy.eu1
irissv	1.0.5	irissv	Refine insertion sequences			29		samtools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
iqtree	2.4.0	iqtree	Efficient phylogenomic software by maximum likelihood	Phylogenetics	Phylogenetic analysis Sequence analysis	79001	iqtree	iqtree		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ipfp_normalisation	0.1.0+galaxy0	ipfp_norm	Normalisation algorithm used to adjust matrices iteratively to satisfy specific row and column sum constraints while preserving the data structure.			0		numpy		To update
intervene	0.6.5	intervene_pairwise intervene_upset	Create pairwise and upset plots	Computational biology	Sequence comparison Sequence visualisation	6418	intervene	intervene		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2 UseGalaxy.or2
interval2maf	1.0.1+galaxy1	Interval2Maf1	Extract MAF blocks given a set of intervals	Sequence analysis		19740	bx-python	bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
interproscan	5.59-91.0	interproscan	Interproscan queries the interpro database and provides annotations.	Gene and protein families Sequence analysis	Sequence motif recognition Protein feature detection	84530	interproscan_ebi	interproscan		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
intermine_galaxy_exchange	0.0.1	galaxy_intermine_exchange	InterMine Exporter			263		coreutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
integronfinder	2.0.5	integron_finder	"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"	Functional genomics Mobile genetic elements Molecular biology Sequence analysis	Nucleic acid feature detection Sequence motif recognition Protein feature detection Genome annotation	72347	integron_finder	integron_finder		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
instrain	1.5.3	instrain_compare instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	Mapping Metagenomics	SNP detection Genome comparison	106	instrain	instrain		To update	UseGalaxy.cz2 UseGalaxy.eu2
infercnv	1.22.0	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data		Heat map generation Expression analysis RNA-Seq analysis Copy number variation detection Clustering	29	infercnv	bioconductor-infercnv		Up-to-date	UseGalaxy.eu1
iedb_api	2.15.2	iedb_api	Get epitope binding predictions from IEDB-API			1590		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
idr_download_by_ids	0.45	idr_download_by_ids	Image Data Resource downloading tool			639		omero-py		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
idr	2.0.3	idr	Galaxy wrappers for the IDR package from Nathan Boleu			4931		idr		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
idba		idba_hybrid idba_tran idba_ud	Wrappers for the idba assembler variants.	Sequence assembly	Sequence assembly	2938	idba	idba		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
icescreen	1.3.3	icescreen	identification of ICEs and IMEs in Bacillota genomes.	Mobile genetic elements Sequence sites, features and motifs Genomics Molecular interactions, pathways and networks Structural variation	Database search Protein feature detection	0	icescreen	icescreen		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
hypo	1.0.3	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	Sequence assembly Genomics	Optimisation and refinement Genome assembly	505	HyPo	hypo		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
hyphy	2.5.47	hyphy_absrel hyphy_annotate hyphy_bgm hyphy_busted hyphy_cfel hyphy_conv hyphy_fade hyphy_fel hyphy_fubar hyphy_gard hyphy_meme hyphy_prime hyphy_relax hyphy_slac hyphy_sm19 hyphy_strike_ambigs hyphy_summary	Hypothesis Testing using Phylogenies	Phylogeny Small molecules Molecular interactions, pathways and networks	Statistical calculation	20949	HyPhy	hyphy		To update	UseGalaxy.be12 UseGalaxy.cz17 UseGalaxy.eu17 UseGalaxy.fr2 UseGalaxy.no12 UseGalaxy.or2
hybpiper	2.1.6	hybpiper	Analyse targeted sequence capture data	Phylogenetics Plant biology Gene transcripts Sequence assembly Phylogenomics	Sequence trimming Sequence assembly Read mapping	1778	HybPiper	hybpiper		To update	UseGalaxy.eu1 UseGalaxy.or1
humann	3.9	humann humann_barplot humann_join_tables humann_reduce_table humann_regroup_table humann_rename_table humann_renorm_table humann_split_stratified_table humann_split_table humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	Metagenomics Phylogenomics	Species frequency estimation Taxonomic classification Phylogenetic analysis	36509	humann	humann		Up-to-date	UseGalaxy.be1 UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr10 UseGalaxy.no10 UseGalaxy.or10
htseq_count	2.0.9	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	Sequence analysis	Nucleic acid sequence analysis	587449	htseq	htseq		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
data_manager_homer_preparse	4.11	homer_annotatePeaks homer_findMotifs homer_findMotifsGenome homer_gtf_to_annotations homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.		Sequence motif discovery	10287	homer	homer		To update	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr4
hmmer3	3.4	hmmer_alimask hmmer_hmmalign hmmer_hmmbuild hmmer_hmmconvert hmmer_hmmemit hmmer_hmmfetch hmmer_hmmscan hmmer_hmmsearch hmmer_jackhmmer hmmer_nhmmer hmmer_nhmmscan hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	Sequence analysis Sequence sites, features and motifs Gene and protein families	Formatting Multiple sequence alignment Sequence profile generation Format validation Conversion Sequence generation Data retrieval Statistical calculation Database search Formatting Database search Database search Probabilistic sequence generation Statistical calculation Statistical calculation Sequence database search Formatting Sequence database search Database search Sequence database search	43031	hmmer3	hmmer		Up-to-date	UseGalaxy.be12 UseGalaxy.cz12 UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.no12 UseGalaxy.or12
hivclustering	1.3.1	hivclustering	Infers transmission networks from pairwise distances inferred by tn93			0		python-hivclustering		To update
hisat2	2.2.1	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	RNA-seq	Sequence alignment	1504469	hisat2	hisat2		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
hifiasm_meta	0.3.1	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	Sequence assembly Metagenomics	Sequence assembly	457	hifiasm-meta	hifiasm_meta		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
hifiasm	0.25.0	hifiasm	A fast haplotype-resolved de novo assembler			6697		hifiasm		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
hicstuff	3.2.4	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices			0		hicstuff		Up-to-date
hicexplorer	3.7.6	hicexplorer_chicaggregatestatistic hicexplorer_chicdifferentialtest hicexplorer_chicexportdata hicexplorer_chicplotviewpoint hicexplorer_chicqualitycontrol hicexplorer_chicsignificantinteractions hicexplorer_chicviewpoint hicexplorer_chicviewpointbackgroundmodel hicexplorer_hicadjustmatrix hicexplorer_hicaggregatecontacts hicexplorer_hicaverageregions hicexplorer_hicbuildmatrix hicexplorer_hicbuildmatrixmicroc hicexplorer_hiccomparematrices hicexplorer_hiccompartmentspolarization hicexplorer_hicconvertformat hicexplorer_hiccorrectmatrix hicexplorer_hiccorrelate hicexplorer_hicdetectloops hicexplorer_hicdifferentialtad hicexplorer_hicfindrestrictionsites hicexplorer_hicfindtads hicexplorer_hichyperoptDetectLoops hicexplorer_hicinfo hicexplorer_hicinterintratad hicexplorer_hicmergedomains hicexplorer_hicmergeloops hicexplorer_hicmergematrixbins hicexplorer_hicnormalize hicexplorer_hicpca hicexplorer_hicplotaverageregions hicexplorer_hicplotdistvscounts hicexplorer_hicplotmatrix hicexplorer_hicplotsvl hicexplorer_hicplotviewpoint hicexplorer_hicquickqc hicexplorer_hicsummatrices hicexplorer_hictransform hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.			75887		hicexplorer		Up-to-date	UseGalaxy.be33 UseGalaxy.cz35 UseGalaxy.eu39 UseGalaxy.fr4 UseGalaxy.no33 UseGalaxy.or38
hgvsparser	0.1.0	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard			6353		r-base		To update	UseGalaxy.eu1
heinz	1.0	heinz_bum heinz heinz_scoring heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	Genetics Gene expression Molecular interactions, pathways and networks	Pathway or network analysis	3831	heinz	bioconductor-bionet		To update	UseGalaxy.be4 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.no4 UseGalaxy.or4
ggplot2_heatmap2	3.2.0	ggplot2_heatmap2	heatmap.2 function from the R gplots package			143397		r-gplots		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
happy	0.3.14	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	Genomics DNA polymorphism	Variant calling Sequence analysis Genotyping	0	hap.py	hap.py		To update
hapog	1.3.8	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	Sequence assembly Genomics	Genome assembly Optimisation and refinement	1003	hapog	hapog		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
hapcut2	1.3.4	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies		Haplotype mapping Variant classification	123	hapcut2	hapcut2		Up-to-date	UseGalaxy.or1
bio_hansel	2.6.1	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Whole genome sequencing DNA polymorphism Genotype and phenotype Infectious disease Agricultural science	Genotyping SNP detection Genome assembly	737	Biohansel	bio_hansel		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
hamronization	1.1.4	hamronize_summarize hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	Public health and epidemiology Microbiology Bioinformatics	Data handling Antimicrobial resistance prediction Parsing	9491	hamronization	hamronization		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2
halfdeep	0.1.0	halfdeep	HalfDeep: Automated detection of intervals covered at half depth by sequenced reads.			48		halfdeep		Up-to-date	UseGalaxy.or1
gwastools	0.1.0	gwastools_manhattan_plot		GWAS study	Deposition Analysis Annotation	21	gwastools	bioconductor-gwastools		To update	UseGalaxy.fr1 UseGalaxy.no1
gvcftools	0.1	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.			0		gvcftools		To update
gubbins	3.2.1	gubbins	Gubbins - bacterial recombination detection	Phylogeny Genotype and phenotype Whole genome sequencing	Genotyping Phylogenetic inference Ancestral reconstruction	10253	gubbins	gubbins		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
gtftobed12	357	gtftobed12	Convert GTF files to BED12 format	Sequence analysis		21804	UCSC_Genome_Browser_Utilities	ucsc-gtftogenepred		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
gtdbtk	2.4.1	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.	Metagenomics Taxonomy Phylogenetics Database management Proteins	Genome alignment Taxonomic classification Sequence assembly Query and retrieval	2418	GTDB-Tk	gtdbtk		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	Computational biology	Data handling Mapping Generation	449	gtdb_to_taxdump	gtdb_to_taxdump		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
groot	1.1.2	groot	GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples	Metagenomics Microbiology Genomics	Antimicrobial resistance prediction	32	groot	groot		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
graphlan		graphlan graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	Metagenomics Phylogenetics Phylogenomics Cladistics	Phylogenetic inference Phylogenetic tree visualisation Phylogenetic tree editing Taxonomic classification	14929	graphlan	graphlan		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
graphembed	2.4	graphembed	Compute a 2D embedding of a data matrix given supervised class information			208		graph_embed		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
gprofiler	@TOOL_VERSION@+galaxy11	gprofiler_convert gprofiler_gost gprofiler_orth gprofiler_random gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more			12462		r-gprofiler2		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5 UseGalaxy.or5
goseq	1.50.0	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	RNA-Seq	Gene functional annotation	58501	goseq	bioconductor-goseq		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
goenrichment	2.0.1	goenrichment goslimmer	Performs GO Enrichment analysis.	Transcriptomics	Gene-set enrichment analysis	16687	goenrichment	goenrichment		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
gemini	3.02	glimmer_acgt_content glimmer_build_icm glimmer_extract glimmer_gbk_to_orf glimmer_glimmer_to_gff glimmer_long_orfs glimmer_knowledge_based glimmer_not_knowledge_based	Glimmer makes gene predictions.	Sequence analysis	Sequence analysis Genetic variation analysis	4543	gemini	glimmer		Up-to-date	UseGalaxy.be4 UseGalaxy.cz4 UseGalaxy.eu4
ggupset	1.0	emc-ggupset	Create Upset Plots with ggupset			0		r-ggupset		To update
ggplot2	3.5.1	ggplot2_barplot ggplot2_boxplot ggplot2_heatmap ggplot2_pca ggplot2_histogram ggplot2_point ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	Data visualisation	Visualisation	69020	ggplot2	r-ggplot2		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or5
gffread	0.12.7	gffread	gffread filters and/or converts GFF3/GTF2 records	Nucleic acids Sequence analysis	Sequence annotation	46498	gffread	gffread		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
gffcompare	0.12.10	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	Nucleic acids Sequence analysis	Sequence annotation	14587	gffcompare	gffcompare		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
gff3_rebase	1.2	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)			1532		bcbiogff		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
gfa_to_fa	0.1.2	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format			18620				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
getorganelle	1.7.7.1	get_annotated_regions_from_gb get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	Cell biology Sequence assembly Whole genome sequencing Plant biology Model organisms	De-novo assembly Genome assembly Mapping assembly Mapping Sequence trimming	3823	getorganelle	getorganelle		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.or2
get_hrun	0.5.9.2	get_hrun	Annotate indel variants with homopolymer context			9		pyfaidx		To update	UseGalaxy.cz1 UseGalaxy.eu1
geopandas	1.1.1	geopandas_table2geojson	GeoPandas is an open source project to make working with geospatial data easier.			0		geopandas		To update	UseGalaxy.eu1
genrich	0.5+galaxy2	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).			7256		genrich		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
genomic_super_signature	1.2.0	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	RNA-Seq Transcriptomics Microbial ecology Genotype and phenotype Microarray experiment	Gene-set enrichment analysis Essential dynamics Deposition Principal component visualisation Dimensionality reduction	55	genomicsupersignature	bioconductor-genomicsupersignature		To update	UseGalaxy.cz1 UseGalaxy.eu1
genomescope	2.0.1	genomescope	Analyze unassembled short reads			8540		genomescope2		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
genetrack		genetrack	Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.			670		numpy		To update	UseGalaxy.or1
geneiobio	4.7.1+galaxy1	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.			245				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
genehunter_modscore	3.0.0	genehunter_modscore	Maximised LOD score pedigree analysis utility			0		ghm		To update
genebed_maf_to_fasta	1.0.1+galaxy0	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals			2909				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
gemini	0.20.1	gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_db_info gemini_@BINARY@ gemini_@BINARY@ gemini_inheritance gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@ gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	Sequence analysis	Sequence analysis Genetic variation analysis	11577	gemini	gemini		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
gem_tools	0.29.1	gem_check_memote gem_escher_visualization gem_extract_exchange gem_flux_distribution gem_flux_variability_analysis gem_knockout gem_phenotype_phase_plane	Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries.			0		cobra		To update	UseGalaxy.eu4 UseGalaxy.or7
gecko	1.2	gecko	Ungapped genome comparison			1753		gecko		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
gdcwebapp	1.0.0	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format			0		python		To update	UseGalaxy.be1 UseGalaxy.eu1
gatk4_mutect2	4.1.7.0	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK			13833		gatk4		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
gamma	2.2	gamma_s gamma	Gene Allele Mutation Microbial Assessment			0		GAMMA		Up-to-date
funannotate	1.8.17	funannotate_annotate funannotate_clean funannotate_compare funannotate_predict funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	Genomics	Genome annotation	20216	funannotate			To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.or5
duplex_family_size_distribution	1.0.2	fsd fsd_beforevsafter fsd_regions td	Tool that plots a histogram of sizes of read families			602		matplotlib		To update	UseGalaxy.or4
freyja	2.0.0	freyja_aggregate_plot freyja_boot freyja_demix freyja_variants	lineage abundances estimation	Metagenomics	RNA-Seq quantification	24846	freyja	freyja		To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.or2
control_freec	11.6	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	DNA structural variation Oncology Human genetics Data mining	Copy number estimation Variant calling Genome alignment	1528	freec	gawk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
freebayes	1.3.10	freebayes bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	Genomics Genetic variation Rare diseases	Variant calling Statistical calculation	479485	freebayes	freebayes		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
fraggenescan		fraggenescan	Tool for finding (fragmented) genes in short read	Genetics Sequence analysis	Gene prediction	2671	fraggenescan	fraggenescan		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
flash	1.2.11	flash	Fast Length Adjustment of SHort reads	Sequencing Sequence assembly	Read pre-processing Sequence merging Sequence assembly	43194	flash	flash		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
flair	1.5	flair_collapse flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.			2009		flair		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2
filtlong	0.3.0	filtlong	Filtlong - Filtering long reads by quality		Filtering Sequencing quality control	111004	filtlong	filtlong		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fgsea	1.8.0+galaxy1	fgsea	Perform gene set testing using fgsea	Genetics	Gene-set enrichment analysis	31468	fgsea	bioconductor-fgsea		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fermikit	r193	fermi2 fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.			0		fermi2		Up-to-date
feelnc	0.2.1	feelnc	Galaxy wrapper for FEELnc	RNA-seq Functional, regulatory and non-coding RNA	Annotation Classification	2881	feelnc	feelnc		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
featurecounts	2.1.1	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	RNA-Seq	Read summarisation RNA-Seq quantification	1806783	featurecounts	subread		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasttree	2.1.10	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	Phylogenetics Sequence analysis	Phylogenetic tree generation (from molecular sequences) Phylogenetic tree generation (maximum likelihood and Bayesian methods)	109499	fasttree	fasttree		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastspar	1.0.0	fastspar fastspar_pvalues fastspar_reduce	Tool for rapid and scalable correlation estimation for compositional data.	Metagenomics Microbial ecology		0	FastSpar	fastspar		Up-to-date	UseGalaxy.eu1
fastqe	0.3.1+galaxy0	fastqe	FASTQE	Sequence analysis Sequencing	Sequencing quality control	21008	fastqe	fastqe		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastqc	0.74+galaxy1	fastqc	Read QC reports using FastQC	Sequencing Data quality management Sequence analysis	Sequence composition calculation Sequencing quality control Statistical calculation	6372191	fastqc	fastqc		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastq_dl	3.0.1	fastq_dl	Download FASTQ files from ENA.			148		fastq-dl		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
fastplong	0.4.1	fastplong	Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).			0		fastplong		Up-to-date	UseGalaxy.eu1 UseGalaxy.or1
fastp	1.0.1	fastp	Fast all-in-one preprocessing for FASTQ files	Sequence analysis Probes and primers	Sequencing quality control Sequence contamination filtering	1778285	fastp	fastp		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fastk	1.1.0	fastk_fastk fastk_histex fastk_logex	FastK: A K-mer counter (for HQ assembly data sets)	Genomics Sequence analysis	k-mer counting Sequence analysis	168	fastk	fastk		Up-to-date	UseGalaxy.eu3 UseGalaxy.or3
fastani	1.3	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	Microbiology Genetic variation	Genome alignment Sequence similarity search	26914	fastani	fastani		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_stats	2.0	fasta-stats	Display summary statistics for a fasta file.			106138		numpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_nucleotide_color_plot	1.0.1	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.			1240		openjdk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
fargene	0.1	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	Metagenomics Microbiology Public health and epidemiology Antimicrobial resistance	Antimicrobial resistance prediction	1901	fargene	fargene		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
falco	1.2.4	falco	A high throughput sequence QC analysis tool	Workflows Mapping Imaging	Sequencing quality control Visualisation Read mapping	6198	falco	falco		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
fairy	0.5.8	fairy_cov fairy_sketch	Fast approximate contig coverage for metagenomic binning	Metagenomics	Read binning Sequence assembly validation	13	fairy	fairy		Up-to-date	UseGalaxy.eu2
extract_genomic_dna	3.0.3+galaxy3	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.			274193		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
export2graphlan	0.20	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	Taxonomy Metabolomics Biomarkers	Conversion	7678	export2graphlan	export2graphlan		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
exonerate	2.4.0	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	Sequence analysis Sequence sites, features and motifs Molecular interactions, pathways and networks	Pairwise sequence alignment Protein threading Genome alignment	3882	exonerate	exonerate		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
exomedepth	1.1.0	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	Exome sequencing Gene transcripts Mapping Sequencing Genetic variation Rare diseases	Sequence analysis Variant calling Genotyping Copy number estimation	3638	exomedepth	r-exomedepth		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
evidencemodeler	2.1.0	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	Gene expression Gene structure	Gene prediction	9	EvidenceModeler	evidencemodeler		Up-to-date	UseGalaxy.eu1
eukrep	0.6.7	eukrep	Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets	Metagenomics	Nucleic acid sequence analysis	0	eukrep	eukrep		Up-to-date
ete_treeviewer	3.1.3	ete_treeviewer	A toolkit for the analysis and visualization of trees.	Phylogenetics	Phylogenetic analysis Phylogenetic tree editing	0	ete	curl		To update	UseGalaxy.eu1 UseGalaxy.fr1
episcanpy	0.3.2	episcanpy_build_matrix episcanpy_cluster_embed episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	Epigenomics Cell biology DNA	Enrichment analysis Imputation	1689	episcanpy	episcanpy		To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.or3
ensembl_vep	114.2	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions			3475		ensembl-vep		To update	UseGalaxy.cz1 UseGalaxy.eu1
enasearch		enasearch_retrieve_analysis_report enasearch_retrieve_data enasearch_retrieve_run_report enasearch_retrieve_taxons enasearch_search_data	A Python library for interacting with ENA's API			2361		enasearch		To update	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5
ena_webin_cli	8.1.1	ena_webin_cli	Submits a genome assembly to the European Nucleotide Archive (ENA) using the Webin-CLI Submission tool.			0		ena-webin-cli		To update	UseGalaxy.be1 UseGalaxy.eu1
ena_upload	0.9.0	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA).			1909		ena-upload-cli		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
emboss_5	5.0.0	EMBOSS: antigenic1 EMBOSS: backtranseq2 EMBOSS: banana3 EMBOSS: biosed4 EMBOSS: btwisted5 EMBOSS: cai6 EMBOSS: cai_custom6 EMBOSS: chaos7 EMBOSS: charge8 EMBOSS: checktrans9 EMBOSS: chips10 EMBOSS: cirdna11 EMBOSS: codcmp12 EMBOSS: coderet13 EMBOSS: compseq14 EMBOSS: cpgplot15 EMBOSS: cpgreport16 EMBOSS: cusp17 EMBOSS: cutseq18 EMBOSS: dan19 EMBOSS: degapseq20 EMBOSS: descseq21 EMBOSS: diffseq22 EMBOSS: digest23 EMBOSS: dotmatcher24 EMBOSS: dotpath25 EMBOSS: dottup26 EMBOSS: dreg27 EMBOSS: einverted28 EMBOSS: epestfind29 EMBOSS: equicktandem31 EMBOSS: est2genome32 EMBOSS: etandem33 EMBOSS: extractfeat34 EMBOSS: extractseq35 EMBOSS: freak36 EMBOSS: fuzznuc37 EMBOSS: fuzzpro38 EMBOSS: fuzztran39 EMBOSS: garnier40 EMBOSS: geecee41 EMBOSS: getorf42 EMBOSS: helixturnhelix43 EMBOSS: hmoment44 EMBOSS: iep45 EMBOSS: infoseq46 EMBOSS: isochore47 EMBOSS: lindna48 EMBOSS: marscan49 EMBOSS: maskfeat50 EMBOSS: maskseq51 EMBOSS: matcher52 EMBOSS: megamerger53 EMBOSS: merger54 EMBOSS: msbar55 EMBOSS: needle56 EMBOSS: newcpgreport57 EMBOSS: newcpgseek58 EMBOSS: newseq59 EMBOSS: noreturn60 EMBOSS: notseq61 EMBOSS: nthseq62 EMBOSS: octanol63 EMBOSS: oddcomp64 EMBOSS: palindrome65 EMBOSS: pasteseq66 EMBOSS: patmatdb67 EMBOSS: pepcoil68 EMBOSS: pepinfo69 EMBOSS: pepnet70 EMBOSS: pepstats71 EMBOSS: pepwheel72 EMBOSS: pepwindow73 EMBOSS: pepwindowall74 EMBOSS: plotcon75 EMBOSS: plotorf76 EMBOSS: polydot77 EMBOSS: preg78 EMBOSS: prettyplot79 EMBOSS: prettyseq80 EMBOSS: primersearch81 EMBOSS: revseq82 EMBOSS: seqmatchall83 EMBOSS: seqret84 EMBOSS: showfeat85 EMBOSS: shuffleseq87 EMBOSS: sigcleave88 EMBOSS: sirna89 EMBOSS: sixpack90 EMBOSS: skipseq91 EMBOSS: splitter92 EMBOSS: supermatcher95 EMBOSS: syco96 EMBOSS: tcode97 EMBOSS: textsearch98 EMBOSS: tmap99 EMBOSS: tranalign100 EMBOSS: transeq101 EMBOSS: trimest102 EMBOSS: trimseq103 EMBOSS: twofeat104 EMBOSS: union105 EMBOSS: vectorstrip106 EMBOSS: water107 EMBOSS: wobble108 EMBOSS: wordcount109 EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	Molecular biology Sequence analysis Biology	Sequence analysis Local alignment Sequence alignment analysis Global alignment Sequence alignment	601921	emboss	emboss		To update	UseGalaxy.be107 UseGalaxy.cz107 UseGalaxy.eu107 UseGalaxy.fr107 UseGalaxy.no107 UseGalaxy.or107
emboss	6.6.0	emboss_needle emboss_needleall	Galaxy wrappers for EMBOSS6 tools	Molecular biology Sequence analysis Biology	Sequence analysis Local alignment Sequence alignment analysis Global alignment Sequence alignment	2	emboss	emboss		Up-to-date	UseGalaxy.eu2
egsea	1.20.0	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	Systems biology	Gene set testing	10922	egsea	bioconductor-egsea		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
edger	3.36.0	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	Genetics RNA-Seq ChIP-seq	Differential gene expression analysis	93817	edger	bioconductor-edger		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ebi_tools	0.1.1	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases			1880		six		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
drug2cell	0.1.2	drug2cell	Collection of utility functions for gene group activity evaluation in scanpy.			0		drug2cell		Up-to-date	UseGalaxy.eu1
dropletutils	1.10.0	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	Gene expression RNA-seq Sequencing Transcriptomics	Loading Community profiling	11501	dropletutils	bioconductor-dropletutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
drep	3.6.2	drep_compare drep_dereplicate	dRep compares and dereplicates genome sets	Metagenomics Genomics Sequence analysis	Genome comparison	1572	drep	drep		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
dram	1.5.0	dram_annotate dram_distill dram_merge_annotations dram_neighborhoods dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	Metagenomics Biological databases Molecular genetics	Gene functional annotation	7707	dram	dram		Up-to-date	UseGalaxy.cz5 UseGalaxy.eu5
dos2unix	7.5.2	dos2unix	dos2unix convert text files with DOS or Mac line breaks to Unix line breaks and vice versa.			0		dos2unix		To update	UseGalaxy.eu1
dnaweaver	1.0.2	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.			0		dnaweaver_synbiocad		Up-to-date
dnabot	3.1.0	dnabot	DNA assembly using BASIC on OpenTrons			0		dnabot		To update
disco		disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	Structure determination	Protein sequence analysis	1876	disco	disco		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
dimet	0.2.4	dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@ dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.			0		dimet		Up-to-date
diffdock	1.1.3	diffdock	Diffusion Steps, Twists, and Turns for Molecular Docking.			0				To update	UseGalaxy.eu1
diffbind	3.12.0	diffbind	Diffbind provides functions for processing ChIP-Seq data.	ChIP-seq	Differential binding analysis	30194	diffbind	bioconductor-diffbind		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
diamond	2.1.13	bg_diamond bg_diamond_makedb bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	Sequence analysis Proteins	Sequence alignment analysis	161526	diamond	diamond		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
dexseq	1.48.0	dexseq dexseq_count plotdexseq	Inference of differential exon usage in RNA-Seq	RNA-Seq	Enrichment analysis Exonic splicing enhancer prediction	51988	dexseq	bioconductor-dexseq		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
deseq2	2.11.40.8	deseq2	Differential gene expression analysis based on the negative binomial distribution	RNA-Seq	Differential gene expression analysis RNA-Seq analysis	407449	DESeq2	bioconductor-deseq2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
delly	0.9.1	delly_call delly_classify delly_cnv delly_filter delly_lr delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	DNA structural variation Sequencing Pathology Genomics Genetic variation Bioinformatics Population genomics Rare diseases	Indel detection Structural variation detection Variant calling Genotyping Genetic variation analysis	1823	delly2	delly		To update	UseGalaxy.be6 UseGalaxy.cz6 UseGalaxy.eu6
deg_annotate	1.1.0+galaxy1	deg_annotate	Annotate DESeq2/DEXSeq output tables		RNA-Seq analysis Gene functional annotation	67834	deg_annotate	bedtools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
deepvariant	1.5.0	deepvariant	DeepVariant is a deep learning-based variant caller			8283				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
deepsig	1.2.5	deepsig	Predictor of signal peptides in proteins based on deep learning			182		deepsig		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
deepmicro	1.4	deepmicro	Representation learning and classification framework	Microbial ecology Machine learning Pathology Public health and epidemiology Allergy, clinical immunology and immunotherapeutics	Essential dynamics Splitting Community profiling	559	DeepMicro	deepmicro		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
deeparg	1.0.4	deeparg_predict deeparg_short_reads	A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes	Microbiology	Antimicrobial resistance prediction Antimicrobial resistance prediction	0	deeparg	deeparg		Up-to-date	UseGalaxy.eu2 UseGalaxy.fr2
decontaminator	1.0.0	decontaminator	Deep Learning method for novel virus detection in sequencing data	Metagenomics	Filtering	136	decontaminator	numpy		To update	UseGalaxy.cz1 UseGalaxy.eu1
decontam	1.22.0	decontam	Removes decontamination features (ASVs/OTUs) using control samples	Metagenomics Microbial ecology Sequencing	Classification	1	decontam	bioconductor-decontam		To update	UseGalaxy.eu1
datamash	1.9	datamash_ops datamash_reverse datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.			979675		datamash		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
data_source_iris_tcga	1.0.0	data_source_iris_tcga	IRIS-TCGA Data source tool			0		python		To update
das_tool	1.1.7	Fasta_to_Contig2Bin das_tool	DAS Tool for genome resolved metagenomics	Metagenomics	Read binning	5527	dastool	das_tool		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
dada2	1.34.0	dada2_assignTaxonomyAddspecies dada2_dada dada2_filterAndTrim dada2_learnErrors dada2_makeSequenceTable dada2_mergePairs dada2_plotComplexity dada2_plotQualityProfile dada2_primerCheck dada2_removeBimeraDenovo dada2_seqCounts	DADA2 wrappers	Sequencing Genetic variation Microbial ecology Metagenomics	Variant calling DNA barcoding	379190	dada2	bioconductor-dada2		Up-to-date	UseGalaxy.be10 UseGalaxy.cz10 UseGalaxy.eu11 UseGalaxy.fr11 UseGalaxy.no10 UseGalaxy.or10
cwpair2	1.1.1	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.			281		matplotlib		To update	UseGalaxy.or1
cutesv	2.1.2	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	DNA structural variation Sequencing Computer science	Split read mapping Genotyping Structural variation detection	424	cuteSV	cutesv		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
cutadapt	5.1	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	Genomics Probes and primers Sequencing	Sequence trimming Primer removal Read pre-processing	817890	cutadapt	cutadapt		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
crossmap	0.7.3	crossmap_bam crossmap_bed crossmap_bw crossmap_gff crossmap_region crossmap_vcf crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies			7755		crossmap		Up-to-date	UseGalaxy.be5 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.no5 UseGalaxy.or5
crosscontamination_barcode_filter	0.3	crosscontamination_barcode_filter	Barcode contamination discovery tool		Filtering Sequence contamination filtering Sequencing quality control RNA-Seq analysis	553	cross-contamination_barcode_filter	r-ggplot2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
crispr_studio	1+galaxy0	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	Sequence analysis Genomics Data visualisation	Visualisation	2090	crisprstudio	crispr_studio		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
cramino	1.1.0	cramino	A tool for quick quality assessment of cram and bam files, intended for long read sequencing.			0		cramino		Up-to-date
coverm	0.7.0	coverm_contig coverm_genome	CoverM genome and contig wrappers	Metagenomics Sequence analysis	Local alignment	1917	coverm	coverm		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
coverage_report	0.0.4	CoverageReport2	Generate Detailed Coverage Report from BAM file			0		perl-number-format		To update
cosg	1.0.1	cosg	Marker gene identification for single-cell sequencing data using COSG.	Bioinformatics	Nucleic acid sequence analysis	0	cosg	cosg		To update	UseGalaxy.eu1
coreprofiler	1.1.3	coreprofiler_allele_calling	CoreProfiler, a tool for cgMLST allele calling from bacterial genome assemblies	Microbiology Bioinformatics Phylogenetics	Multilocus sequence typing	0	coreprofiler	coreprofiler		To update	UseGalaxy.eu1 UseGalaxy.fr1
concoct	1.1.0	concoct concoct_coverage_table concoct_cut_up_fasta concoct_extract_fasta_bins concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	Metagenomics	Sequence clustering Read binning	8370	concoct	concoct		Up-to-date	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.or5
compress_file	0.1.0	compress_file	Compress files.			25921		gzip		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
compose_text_param	0.1.1	compose_text_param	Compose a text parameter value using text, integer and float values			60897				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
compleasm	0.2.6	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	Sequence assembly Genomics Transcriptomics Sequence analysis	Sequence assembly validation	995	compleasm	compleasm		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
comebin	1.0.4	comebin	Binning of metagenomic contigs using COntrastive Multi-viEw representation learning			0		comebin		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
column_remove_by_header	1.0	column_remove_by_header	Remove columns by header			17627		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
column_order_header_sort	0.0.1	column_order_header_sort	Sort Column Order by heading			6596		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
column_maker	2.1	Add_a_column1	Compute an expression on every row			4769937		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
collection_element_identifiers	0.0.2	collection_element_identifiers	Extract element identifiers of a collection			21953				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
collection_column_join	0.0.3	collection_column_join	Column Join on Collections			61363		coreutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
colibread	24.7.14	commet discosnp_rad discosnp_pp kissplice lordec mapsembler2 takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome			1626		commet		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
colabfold	1.5.5	colabfold_alphafold colabfold_msa	Protein prediction based on AlphaFold2	Protein folds and structural domains Protein folding, stability and design Structure prediction Sequence sites, features and motifs Metagenomics	Database search Protein structure prediction Fold recognition	9177	Colabfold			To update	UseGalaxy.or2
cojac	0.9.3	cooc_mutbamscan cooc_pubmut cooc_tabmut	co-occurrence of mutations on amplicons	Genetic variation		2779	cojac	cojac		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.or2
codeml	4.9	codeml	Detects positive selection	Phylogenetics Sequence analysis	Probabilistic sequence generation Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetic tree analysis	62370	paml	paml		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
cnvkit	0.9.12	cnvkit_access cnvkit_antitarget cnvkit_autobin cnvkit_batch cnvkit_export_bed cnvkit_breaks cnvkit_call cnvkit_export_cdt cnvkit_coverage cnvkit_diagram cnvkit_fix cnvkit_genemetrics cnvkit_heatmap cnvkit_export_jtv cnvkit_export_nexus_basic cnvkit_export_nexus_ogt cnvkit_reference cnvkit_scatter cnvkit_export_seg cnvkit_segment cnvkit_segmetrics cnvkit_sex cnvkit_target cnvkit_theta cnvkit_export_vcf	detecting copy number variants and alterations genome-wide from high-throughput sequencing	DNA structural variation	Variant calling	1130	cnvkit	cnvkit		Up-to-date	UseGalaxy.cz17 UseGalaxy.eu25 UseGalaxy.fr25 UseGalaxy.or25
cnv-vcf2json	2.0.0	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.			13		cnv-vcf2json		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
cnv_phenopacket	1.0.2	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.			7		cnv-phenopacket		To update	UseGalaxy.eu1
clustering_from_distmat	1.1.1	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy			123		python		To update	UseGalaxy.eu1
clustalw	2.1	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	Phylogeny Sequence analysis	Multiple sequence alignment	195886	clustal2	clustalw		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
clair3	1.0.10	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	Molecular genetics	Variant calling	5081	clair3	clair3		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
cite_seq_count	1.4.4	cite_seq_count	Count CMO/HTO	Transcriptomics Immunoproteins and antigens	RNA-Seq quantification	174	CITE-seq-Count	cite-seq-count		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
circos	0.69.8	circos_aln_to_links circos_binlinks circos_bundlelinks circos circos_gc_skew circos_resample circos_wiggle_to_scatter circos_wiggle_to_stacked circos_tableviewer circos_interval_to_text circos_interval_to_tile	Build Circos Plots in Galaxy		Sequence visualisation	91641	galactic_circos	circos		To update	UseGalaxy.be11 UseGalaxy.cz11 UseGalaxy.eu11 UseGalaxy.fr11 UseGalaxy.no11 UseGalaxy.or11
circexplorer2	2.3.8	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	RNA splicing Gene transcripts Literature and language		806	circexplorer2	circexplorer2		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
cialign	1.1.4	cialign	Tool to clean, visualise and analyse a multiple sequence alignment			0		cialign		Up-to-date	UseGalaxy.eu1
chromeister	1.5.a	chromeister	ultra-fast pairwise genome comparisons			13108		chromeister		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
chopper	0.10.0	chopper	Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT.			0		chopper		Up-to-date	UseGalaxy.eu1
chopin2	1.0.9.post1	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing			17		chopin2		To update	UseGalaxy.or1
chira	1.4.3	chira_collapse chira_extract chira_map chira_merge chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	RNA Molecular interactions, pathways and networks Functional, regulatory and non-coding RNA		42860	chira	chira		Up-to-date	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.no5 UseGalaxy.or5
chewbbaca		chewbbaca_allelecall chewbbaca_allelecallevaluator chewbbaca_createschema chewbbaca_downloadschema chewbbaca_extractcgmlst chewbbaca_joinprofiles chewbbaca_nsstats chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm			1302		chewbbaca		To update	UseGalaxy.eu8
cherri	0.7	cherri_eval cherri_train	Computational Help Evaluating RNA-RNA interactions	Molecular interactions, pathways and networks Structure analysis Machine learning		207	cherri	cherri		To update	UseGalaxy.cz2 UseGalaxy.eu2
checkm2	1.0.2	checkm2	Rapid assessment of genome bin quality using machine learning	Genomics Phylogenomics Phylogenetics Taxonomy Metagenomics Data quality management	Sequence assembly validation Validation Sequence composition calculation Sequencing quality control Statistical calculation	0	checkm	checkm2		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
checkm	1.2.4	checkm_analyze checkm_lineage_set checkm_lineage_wf checkm_plot checkm_qa checkm_taxon_set checkm_taxonomy_wf checkm_tetra checkm_tree checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	Genomics Phylogenomics Phylogenetics Taxonomy Metagenomics Data quality management	Sequence assembly validation Validation Sequence composition calculation Sequencing quality control Statistical calculation	11964	checkm	checkm-genome		Up-to-date	UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr10 UseGalaxy.or10
charts	1.0.1	charts	Enables advanced visualization options in Galaxy Charts			19379		r-getopt		To update
cemitool	1.30.0	cemitool	Gene co-expression network analysis tool	Gene expression Transcriptomics Microarray experiment	Enrichment analysis Pathway or network analysis	806	cemitool	bioconductor-cemitool		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
cd_hit	4.8.1	cd_hit	Cluster or compare biological sequence datasets	Sequencing	Sequence clustering	13733	cd-hit	cd-hit		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
contig_annotation_tool	5.2.3	cat_add_names cat_bins cat_contigs cat_prepare cat_summarise	Contig Annotation Tool (CAT)	Metagenomics Metagenomic sequencing Taxonomy Sequence assembly	Taxonomic classification Sequence assembly Coding region prediction	18894	cat_bins	cat		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr5 UseGalaxy.no5 UseGalaxy.or2
cami_amber	2.0.7	biobox_add_taxid cami_amber cami_amber_add cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments	Metagenomics	Read binning	8385	cami-amber	cami-amber		Up-to-date	UseGalaxy.eu4 UseGalaxy.or4
calculate_numeric_param	0.1.0	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.			1724				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
calculate_contrast_threshold	1.0.0	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.			0		numpy		To update
cactus	2.7.1	cactus_cactus cactus_export	Cactus is a reference-free whole-genome multiple alignment program	Genomics Sequence analysis Phylogeny Sequence assembly Mapping Phylogenetics	Multiple sequence alignment Genome alignment	2834	cactus			To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr1 UseGalaxy.no2 UseGalaxy.or2
bwameth	0.2.9	bwameth	Fast and accurate alignment of BS-seq reads			21361		bwameth		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
bwa_mem2	2.3	bwa_mem2_idx bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	Mapping	Sequence alignment	152689	bwa-mem2	bwa-mem2		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
bwa	0.7.19	bwa_mem bwa	Wrapper for bwa mem, aln, sampe, and samse	Mapping	Genome indexing Sequence alignment Read mapping Sequence alignment Generation Sequence alignment Generation Sequence alignment Sequence alignment	1858218	bwa	bwa		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
busco	5.8.0	busco	BUSCO assess genome and annotation completeness	Sequence assembly Genomics Transcriptomics Sequence analysis	Sequence assembly validation	209510	busco	busco		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
brew3r_r	1.0.2	brew3r_r	Extend 3' end of a GTF using another GTF as a template	Transcriptomics Genomics	Genome annotation	12	brew3r.r			To update	UseGalaxy.eu1 UseGalaxy.or1
breseq	0.35.5	breseq	Predicts mutations in microbial genomes	Sequencing Sequence analysis DNA mutation	Polymorphism detection	4203	breseq	breseq		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
bracken	3.1	est_abundance	Bayesian Reestimation of Abundance with KrakEN	Metagenomics Microbial ecology	Statistical calculation	104329	bracken	bracken		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
bowtie2	2.5.3	bowtie2	Bowtie2: Fast and sensitive read alignment	Mapping Genomics Mapping	Read mapping	1520871	bowtie2	bowtie2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
blastxml_to_gapped_gff3	1.1	blastxml_to_gapped_gff3	BlastXML to gapped GFF3			1122		bcbiogff		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
magicblast	1.7.0	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome			6951		magicblast		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
biscot	2.3.3	biscot	Bionano scaffolding correction tool			3		biscot		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
bp_genbank2gff3	1.1	bp_genbank2gff3	Converts GenBank format files to GFF3	Genomics Software engineering Data management	Data handling Service invocation	28460	bioperl	perl-bioperl		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
biomformat	2.1.15	biom_add_metadata biom_convert biom_from_uc biom_normalize_table biom_subset_table biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	Laboratory information management Sequence analysis	Formatting	22711	biomformat	biom-format		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu6 UseGalaxy.no1 UseGalaxy.or2
bioinformatics_cafe	0.1.0	fasta_regex_finder	Miscellanea of scripts for bioinformatics			2692		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
bioext	0.21.9	bioext_bam2msa bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!			49510		python-bioext		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.or2
binning_refiner	1.4.3	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	Metagenomics Sequence assembly Microbial ecology	Read binning Sequence clustering	161	binning_refiner	binning_refiner		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
binette	1.1.2	binette	Binning refinement tool	Metagenomics	Read binning	0	binette	binette		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
bigwig_outlier_bed	0.2.4	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files			1564	bigtools	python		To update	UseGalaxy.eu1 UseGalaxy.or1
bigscape	1.1.9	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	Phylogeny Microbial ecology Mapping Metabolomics Bioinformatics Gene and protein families	Clustering Global alignment Fold recognition	1196	BiG-SCAPE	bigscape		Up-to-date	UseGalaxy.eu1
berokka	0.2.3	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.			1024		berokka		Up-to-date	UseGalaxy.or1
bellerophon	1.0	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.			3799		bellerophon		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
bellavista	0.0.2	bellavista_prepare	Open-Source Visualization for Imaging-Based Spatial Transcriptomics			0				To update	UseGalaxy.eu1
bedtools	2.31.1	bedtools_annotatebed bedtools_bamtobed bedtools_bed12tobed6 bedtools_bedtobam bedtools_bedtoigv bedtools_bedpetobam bedtools_closestbed bedtools_clusterbed bedtools_complementbed bedtools_coveragebed bedtools_expandbed bedtools_fisher bedtools_flankbed bedtools_genomecoveragebed bedtools_getfastabed bedtools_groupbybed bedtools_intersectbed bedtools_jaccard bedtools_links bedtools_makewindowsbed bedtools_map bedtools_maskfastabed bedtools_mergebed bedtools_multicovtbed bedtools_multiintersectbed bedtools_nucbed bedtools_overlapbed bedtools_randombed bedtools_reldistbed bedtools_shufflebed bedtools_slopbed bedtools_sortbed bedtools_spacingbed bedtools_subtractbed bedtools_tagbed bedtools_unionbedgraph bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	Genomics	Mapping	1782914	bedtools	bedtools		Up-to-date	UseGalaxy.be37 UseGalaxy.cz37 UseGalaxy.eu37 UseGalaxy.fr37 UseGalaxy.no37 UseGalaxy.or37
bedops_sortbed	2.4.42	bedops-sort-bed	BEDOPS: high-performance genomic feature operations			457		bedops		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
beagle	5.4_29Oct24.c8e	beagle	Beagle is a program for phasing and imputing missing genotypes.			137		beagle		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
beacon2	2.0.0	beacon2_csv2xlsx beacon2_pxf2bff beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	Genetic variation Population genetics Data security Rare diseases	Service discovery Database search Genetic variation analysis	52	ga4gh_beacon	beacon2-ri-tools		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.or3
Beacon2_Import	2.2.4	beacon2_analyses beacon2_biosamples beacon2_bracket beacon2_cnv beacon2_cohorts beacon2_datasets beacon2_gene beacon2_import beacon2_individuals beacon2_range beacon2_runs beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	Genetic variation Population genetics Data security Rare diseases	Service discovery Database search Genetic variation analysis	51	ga4gh_beacon	beacon2-import		Up-to-date	UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.or12
bctools	0.2.2	bctools_convert_to_binary_barcode bctools_extract_crosslinked_nucleotides bctools_extract_alignment_ends bctools_extract_barcodes bctools_merge_pcr_duplicates bctools_remove_tail bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0			3130		bctools		Up-to-date	UseGalaxy.be1 UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.no7
bcftools	1.15.1	bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@_from_vcf bcftools_@EXECUTABLE@_to_vcf bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_plugin_@PLUGIN_ID@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@_list_samples bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@ bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	Genetic variation DNA polymorphism GWAS study Genotyping experiment	Data handling Variant calling	0	bcftools	bcftools		To update
bbtools	39.08	bbtools_bbduk bbtools_bbmap bbtools_bbmerge bbtools_bbnorm bbtools_callvariants bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	Sequencing RNA splicing Whole genome sequencing Phylogenetics Metagenomics RNA-Seq	RNA-Seq analysis Sequence trimming Read mapping Sequence contamination filtering Read binning Sequence alignment	26010	bbmap	bbmap		To update	UseGalaxy.cz4 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.or3
bbgbigwig	0.1	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	Sequence analysis		1082	UCSC_Genome_Browser_Utilities	ucsc-bedgraphtobigwig		To update	UseGalaxy.eu1 UseGalaxy.or1
bayescan	2.1	BayeScan	Detecting natural selection from population-based genetic data	Genetics Evolutionary biology Statistics and probability DNA polymorphism	Statistical inference	104	bayescan	bayescan		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
bax2bam	0.0.11	bax2bam	BAX to BAM converter			420		bax2bam		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
basil	1.2.0	basil	Breakpoint detection, including large insertions			806		anise_basil		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
barrnap	1.2.2	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	Genomics Model organisms Model organisms	Gene prediction	16098	barrnap	barrnap		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
baredsc	1.1.3	baredsc_1d baredsc_2d baredsc_combine_1d baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	RNA-Seq Cytometry Transcriptomics Gene transcripts Statistics and probability	Data retrieval Expression correlation analysis Differential gene expression profiling	315	baredsc	baredsc		Up-to-date	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.or4
barcode_splitter	0.18.4.0	barcode_splitter	A utility to split sequence files using multiple sets of barcodes			0		barcode_splitter		To update
bandage	2022.09	bandage_image bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	Genomics Sequence assembly	Sequence assembly visualisation	151833	bandage	bandage_ng		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
bamutil		bamutil_clip_overlap bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.			436		bamutil		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
bam_to_scidx	1.0.1	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.			919		openjdk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
bakta	1.9.4	bakta	"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."	Genomics Sequence analysis Bioinformatics	Genome annotation	39052	bakta	bakta		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
b2btools	3.0.5+galaxy0	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.		Protein disorder prediction Protein secondary structure prediction Protein feature detection	372	b2btools	b2btools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
autobigs	0.6.2	autobigs-cli	Automated MLST typing from PubMLST and InstitutPasteur.			0	AutoBIGS.CLI	autobigs-cli		To update	UseGalaxy.eu1
augustus	3.5.0	augustus augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	Gene transcripts Gene and protein families	Gene prediction Ab-initio gene prediction Homology-based gene prediction Homology-based gene prediction Operation	45840	augustus	augustus		Up-to-date	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
astral	5.7.8	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees			151		astral-tree		Up-to-date	UseGalaxy.be1
assembly_stats	17.02	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.			26		rjchallis-assembly-stats		Up-to-date	UseGalaxy.fr1
artic	1.7.3	artic_guppyplex artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	Genomics	Sequence alignment	12443	artic	artic		To update	UseGalaxy.be1 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no1 UseGalaxy.or2
art	2014.11.03.0	art_454 art_illumina art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	Bioinformatics	Conversion	259	art	art		To update	UseGalaxy.eu3
arriba	2.5.1	arriba arriba_draw_fusions arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR			4316		arriba		Up-to-date	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.or3
argnorm	1.0.0	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database		Gene functional annotation	76	argnorm	argnorm		To update	UseGalaxy.eu1 UseGalaxy.fr1
annotatemyids	3.18.0	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages		Annotation	113317	annotatemyids	bioconductor-org.hs.eg.db		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
anndata2ri	1.3.2	anndata2ri	Convert between Anndata and SingCellExperiment objects		Data handling	0	anndata2ri	anndata2ri		To update	UseGalaxy.eu1
anndata	0.10.9	anndata_export anndata_import anndata_inspect anndata_manipulate modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects			77315	anndata	anndata		To update	UseGalaxy.be5 UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.fr3 UseGalaxy.no5 UseGalaxy.or5
ancombc	1.4.0	ancombc	Performs analysis of compositions of microbiomes with bias correction.	Microbial ecology Metagenomics Taxonomy	DNA barcoding	37	ancombc	bioconductor-ancombc		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
AMRFinderPlus	3.12.8	amrfinderplus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.	Microbiology Public health and epidemiology Infectious disease	Antimicrobial resistance prediction	19178	amrfinderplus	ncbi-amrfinderplus		To update	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
ampvis2	2.8.9	ampvis2_alpha_diversity ampvis2_boxplot ampvis2_core ampvis2_export_fasta ampvis2_export_otu ampvis2_frequency ampvis2_heatmap ampvis2_load ampvis2_merge_ampvis2 ampvis2_mergereplicates ampvis2_octave ampvis2_ordinate ampvis2_otu_network ampvis2_rankabundance ampvis2_rarecurve ampvis2_setmetadata ampvis2_subset_samples ampvis2_subset_taxa ampvis2_timeseries ampvis2_venn	ampvis2	Biodiversity	Analysis Visualisation	2712	ampvis			To update	UseGalaxy.cz19 UseGalaxy.eu20 UseGalaxy.or1
ampligone	2.0.1	ampligone	AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment.			0		AmpliGone		Up-to-date
amplican	1.14.0	amplican	AmpliCan is an analysis tool for genome editing.	PCR experiment Statistics and probability	Alignment Standardisation and normalisation	84	amplican	bioconductor-amplican		To update	UseGalaxy.cz1 UseGalaxy.eu1
allegro	2	allegro	Linkage and haplotype analysis from deCODE	Sequence analysis Transcription factors and regulatory sites DNA	Sequence motif discovery	0	allegro	allegro		To update
aldex2	1.26.0	aldex2	Performs analysis Of differential abundance taking sample variation into account	Gene expression Statistics and probability	Statistical inference	299	aldex2	bioconductor-aldex2		To update	UseGalaxy.cz1 UseGalaxy.eu1
aegean	0.16.0	aegean_canongff3 aegean_gaeval aegean_locuspocus aegean_parseval	AEGeAn toolkit wrappers	Sequence analysis Gene structure	Sequence annotation	2619	gaeval	aegean		Up-to-date	UseGalaxy.be1 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.or4
add_input_name_as_column	0.2.0	addName	Add input name as column on an existing tabular file			121270		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
adapter_removal	2.3.4	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.		Sequence trimming Sequence merging Primer removal	517	adapterremoval	adapterremoval		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
abyss	2.3.10	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	Sequence assembly	Genome assembly De-novo assembly Scaffolding	9601	abyss	abyss		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
abritamr	1.0.19	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	Microbiology Public health and epidemiology Infectious disease Antimicrobial resistance	Antimicrobial resistance prediction	1663	abritamr	abritamr		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
abricate	1.0.1	abricate abricate_list abricate_summary	Mass screening of contigs for antiobiotic resistance genes	Genomics Microbiology	Antimicrobial resistance prediction	1566054	ABRicate	abricate		Up-to-date	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.no3 UseGalaxy.or3
trimns	0.1.0	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline			48		trimns_vgp		To update	UseGalaxy.cz1 UseGalaxy.eu1
venn_list	0.1.2	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc			24966		galaxy_sequence_utils		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
seq_select_by_id	0.0.15	seq_select_by_id	Select sequences by ID			4227		biopython		To update	UseGalaxy.or1
seq_rename	0.0.10	seq_rename	Rename sequences with ID mapping from a tabular file			0		galaxy_sequence_utils		To update	UseGalaxy.no1
seq_primer_clip	0.0.18	seq_primer_clip	Trim off 5' or 3' primers			0		galaxy_sequence_utils		To update
seq_length	0.0.5	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)			0		biopython		To update
seq_filter_by_mapping	0.0.8	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files			4832		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
seq_filter_by_id	0.2.9	seq_filter_by_id	Filter sequences by ID			77309		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
seq_composition	0.0.5	seq_composition	Sequence composition			2162		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
samtools_idxstats	0.0.6	samtools_idxstats	BAM mapping statistics (using samtools idxstats)			201323		samtools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
samtools_depth	0.0.3	samtools_depth	Coverage depth via samtools			18978		samtools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
samtools_depad	0.0.5	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)			0		samtools		To update
sample_seqs	0.2.6	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)			7307		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
tmhmm_and_signalp	0.0.13	promoter2 Psortb rxlr_motifs signalp3 tmhmm2 wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb			13659		promoter		To update	UseGalaxy.be6 UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.no6
predictnls	0.0.10	predictnls	Python reimplementation of predictNLS for Galaxy			0				To update
nlstradamus	0.0.11	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences			0		NLStradamus		To update
mummer	0.0.8	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot			2052		ghostscript		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
get_orfs_or_cdss	0.2.3	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)			2684		biopython		To update	UseGalaxy.be1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
fastq_paired_unpaired	0.1.5	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads			0		galaxy_sequence_utils		To update
fastq_pair_names	0.0.5	fastq_pair_names	Extract FASTQ paired read names			0		galaxy_sequence_utils		To update
fastq_filter_by_id	0.0.7	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)			0		galaxy_sequence_utils		To update
fasta_filter_by_id	0.0.7	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)			0		galaxy_sequence_utils		To update
effectivet3	0.0.21	effectiveT3	Find bacterial type III effectors in protein sequences	Sequence analysis	Sequence classification	0	effectivet3	effectiveT3		To update
coverage_stats	0.1.0	coverage_stats	BAM coverage statistics using samtools idxstats and depth			0		samtools		To update
count_roi_variants	0.0.6	count_roi_variants	Count sequence variants in region of interest in BAM file			0		samtools		To update
clinod	0.1.0	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	Sequence analysis	Nucleic acid sequence analysis	559	clinod	clinod		To update	UseGalaxy.or1
clc_assembly_cell	0.0.7	clc_assembler clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio			0		samtools		To update
chromosome_diagram	0.0.3	chromosome_diagram	Chromosome Diagrams using Biopython			0		biopython		To update
align_back_trans	0.0.10	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)			588		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
wtdbg	2.5	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	Sequence assembly Sequencing	Genome assembly De-novo assembly	1968	wtdbg2	wtdbg		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
wordcloud	1.9.4	wordcloud	A little word cloud generator in Python.			12		wordcloud		To update	UseGalaxy.eu1 UseGalaxy.or1
whisperx	3.4.2	whisperx	Transcribe audio or video files to text using the OpenAI Whisper and speaker diarization using pyannote audio			0				To update	UseGalaxy.eu1
whisper	20231117	whisper	Transcribe audio or video files to text using the OpenAI Whisper.			234				To update	UseGalaxy.eu1
vt	0.2	vt_@BINARY@ vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.			0		vt		To update
vrhyme	1.1.0	vrhyme	Tool for dereplication and binning virus genomes from metagenomes.	Metagenomics Microbial ecology Model organisms Machine learning Sequence assembly	Scaffolding Read binning Read mapping Sequence trimming	0	vRhyme	vrhyme		Up-to-date	UseGalaxy.eu1
vpt	1.3.0	vpt_extract vpt_segment	Vizgen Post-processing Tool			0				To update	UseGalaxy.eu2
uniprot_rest_interface	0.7	uniprot	UniProt ID mapping and sequence retrieval			9659		requests		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
trim_galore	0.6.10	trim_galore	Trim Galore adaptive quality and adapter trimmer	Sequence analysis	Sequence trimming Primer removal Read pre-processing	738950	trim_galore	trim-galore		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
create_tool_recommendation_model	0.0.5	create_tool_recommendation_model	Create model to recommend tools			522		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tiara	1.0.3	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Sequencing Genomics DNA polymorphism DNA structural variation	Genome comparison Data retrieval Variant calling Genome visualisation Structural variation detection	296	Tiara	tiara		To update	UseGalaxy.eu1
tgsgapcloser	1.0.3	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	Sequencing Sequence assembly Phylogeny Transcription factors and regulatory sites Mapping	Genome assembly Read mapping Scaffolding Localised reassembly	552	TGS-GapCloser	tgsgapcloser		To update	UseGalaxy.cz1 UseGalaxy.eu1
text_processing	9.5	tp_awk_tool tp_cat tp_cut_tool tp_easyjoin_tool tp_find_and_replace tp_grep_tool tp_head_tool tp_multijoin_tool nl tp_text_file_with_recurring_lines tp_replace_in_column tp_replace_in_line tp_sed_tool tp_sort_header_tool tp_sort_rows tp_uniq_tool tp_tac tp_tail_tool tp_unfold_column_tool tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.			5378481		coreutils		To update	UseGalaxy.be19 UseGalaxy.cz20 UseGalaxy.eu20 UseGalaxy.fr20 UseGalaxy.no19 UseGalaxy.or20
split_file_to_collection	0.5.2	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.			34449		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
split_file_on_column	0.6	tp_split_on_column	Split a file on a specific column.			9569		gawk		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
join_files_on_column_fuzzy	1.0.1	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.			3939		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
column_arrange_by_header	0.2	bg_column_arrange_by_header	Column arrange by header name			11739				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
add_line_to_file	0.1.0	add_line_to_file	Adds a text line to the beginning or end of a file.			20235		coreutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
tapscan	4.76+galaxy0	tapscan_classify	Search for transcription associated proteins (TAPs)			38		hmmer		To update	UseGalaxy.eu1 UseGalaxy.or1
tabpfn	2.0.9	tabpfn	Tabular data prediction using TabPFN using Pytorch.			73		tabpfn		To update	UseGalaxy.eu1
sylph	0.8.1	sylph_profile sylph_query	sylph - fast and precise species-level metagenomic profiling with ANIs	Metagenomics	Taxonomic classification	0	sylph	sylph		Up-to-date	UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
stress_ng	0.12.04	stress_ng	stress test a computer system in various selectable ways			62		stress-ng		To update
bg_statistical_hypothesis_testing	0.3	bg_statistical_hypothesis_testing	Tool for computing statistical tests.			365		numpy		To update	UseGalaxy.cz1 UseGalaxy.eu1
splitfasta	0.5.0	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences			6146		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
sklearn	1.0.11.0	sklearn_mlxtend_association_rules sklearn_clf_metrics sklearn_discriminant_classifier sklearn_ensemble sklearn_estimator_attributes sklearn_feature_selection sklearn_fitted_model_eval sklearn_generalized_linear keras_batch_models keras_model_builder keras_model_config keras_train_and_eval sklearn_label_encoder sklearn_lightgbm ml_visualization_ex model_prediction sklearn_model_validation sklearn_nn_classifier sklearn_numeric_clustering sklearn_pairwise_metrics sklearn_pca sklearn_build_pipeline sklearn_data_preprocess sklearn_regression_metrics sklearn_sample_generator sklearn_searchcv sklearn_model_fit scipy_sparse stacking_ensemble_models sklearn_svm_classifier sklearn_to_categorical sklearn_train_test_eval sklearn_train_test_split	Machine Learning tool suite from Scikit-learn			162587				To update	UseGalaxy.be29 UseGalaxy.cz31 UseGalaxy.eu31 UseGalaxy.fr16 UseGalaxy.no27 UseGalaxy.or14
segemehl	0.2.0.4	segemehl	segemehl - short read mapping with gaps			1308		segemehl		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
sed_wrapper	0.0.1	sed_stream_editor	Manipulate your data with the sed command line tool.			2284		sed		To update
sambamba	1.0.1	sambamba_flagstat sambamba_markdup sambamba_merge sambamba_sort	Sambamba: process your BAM data faster!			2714		sambamba		Up-to-date	UseGalaxy.eu4
salmon	1.10.1	alevin salmon salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	RNA-Seq Gene expression Transcriptomics	Sequence composition calculation RNA-Seq quantification Gene expression analysis	235077	salmon	salmon		To update	UseGalaxy.be3 UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr2 UseGalaxy.no3 UseGalaxy.or3
sailfish	0.10.1.1	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data			23247		bzip2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
viennarna	2.2.10	viennarna_kinfold viennarna_kinwalker viennarna_rna2dfold viennarna_rnaaliduplex viennarna_rnaalifold viennarna_rnacofold viennarna_rnadistance viennarna_rnaduplex viennarna_rnaeval viennarna_rnafold viennarna_rnaheat viennarna_rnainverse viennarna_rnalalifold viennarna_rnalfold viennarna_rnapaln viennarna_rnadpdist viennarna_rnapkplex viennarna_rnaplex viennarna_rnaplfold viennarna_rnaplot viennarna_rnasnoop viennarna_rnasubopt viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures			8297		viennarna		To update	UseGalaxy.cz21 UseGalaxy.eu21 UseGalaxy.no21
trna_prediction	0.6	aragorn_trna trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.			8253		aragorn		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2 UseGalaxy.or2
targetfinder	1.7	targetfinder	Plant small RNA target prediction tool			2212		targetfinder		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
sshmm	1.0.7	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data			227		sshmm		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
sortmerna	4.3.6	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	Metatranscriptomics Metagenomics	Sequence similarity search Sequence comparison Sequence alignment analysis	32066	sortmerna	sortmerna		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format			473		selectsequencesfrommsa		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rnaz	2.1.1	rnaz rnaz_annotate rnaz_cluster rnaz_randomize_aln rnaz_select_seqs rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.			43319		rnaz		Up-to-date	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.no6
rnasnp	1.2.0	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs			95		rnasnp		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rnalien	1.3.6	RNAlien	RNAlien unsupervized RNA family model construction			33		rnalien		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rnaformer	1.2.0	infer_rnaformer	RNAformer: RNA secondary structure prediction			76		rnaformer		To update	UseGalaxy.eu1
rnacommender	0.1.1	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.			1082		sam		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rnacode	0.3.2	rbc_rnacode	Analyze the protein coding potential in MSA			1363		rnacode		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rnabob	2.2.1.0	rbc_rnabob	Fast pattern searching for RNA structural motifs			198		rnabob		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rnashapes	3.3.0	RNAshapes	Compute secondary structures of RNA			258		@EXECUTABLE@		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
ribotaper	1.3.1a	ribotaper_create_annotation ribotaper_create_metaplots ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	Functional genomics	Gene expression profiling	740	ribotaper	ribotaper		To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.no3
remurna	1.0.0	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation			66		remurna		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
reago	1.1	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly RNA Metagenomics Microbiology	Sequence assembly	1	reago	reago		Up-to-date	UseGalaxy.eu1
rcas	1.5.4	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments			1271		bioconductor-rcas		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rbpbench	0.8.1	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	RNA Protein interactions RNA immunoprecipitation Bioinformatics Sequence analysis		109	rbpbench	rbpbench		To update	UseGalaxy.eu1
rrna	0.1	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.			0		hmmsearch3.0		To update
pipmir	0.1.0	pipmir	A method to identify novel plant miRNA.			312		pipmir		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
paralyzer	1.5	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.			356		paralyzer		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
nastiseq	1.0	nastiseq	A method to identify cis-NATs using ssRNA-seq			42		r-nastiseq		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
mqc	1.9	mqc	Ribosome profiling mapping quality control tool			76		mqc		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
mea	0.6.4.1	mea	Maximum expected accuracy prediction			86		mea		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
locarna	2.0.1	locarna_exparnap locarna_multiple locarna_pairwise locarna_pairwise_p locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs			358		locarna		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
kinwalker			Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.			0				To update
intarna	3.4.1	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.			7713		intarna		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
inforna			INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.			0				To update
infernal	1.1.5	infernal_cmalign infernal_cmbuild infernal_cmpress infernal_cmscan infernal_cmsearch infernal_cmstat	Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.	Sequence sites, features and motifs Structural genomics	Nucleic acid feature detection	116069	infernal	infernal		Up-to-date	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.no6 UseGalaxy.or6
htseq_clip	0.1.0+galaxy0	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets			106		htseq-clip		To update	UseGalaxy.cz1 UseGalaxy.eu1
graphprot	1.1.7+galaxy2	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.			496		graphprot		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
exparna	1.0.1	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.			0		exparna		Up-to-date
dotknot	1.3.1	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence			88		vienna_rna		To update	UseGalaxy.cz1 UseGalaxy.eu1
dot2ct	5.7.a	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)			0		rnastructure		To update
dorina	1.0	dorina_search	data source for RNA interactions in post-transcriptional regulation			1639				To update	UseGalaxy.eu1
dewseq	0.1.0+galaxy0	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data			96		python		To update	UseGalaxy.cz1 UseGalaxy.eu1
coprarna	2.1.1	coprarna	Target prediction for prokaryotic trans-acting small RNAs			0		coprarna		To update
compalignp	1.0	compalignp	Compute fractional identity between trusted alignment and test alignment			222		compalignp		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
cofold	2.0.4.0	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.			361		cofold		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
cmv	1.0.8	cmcv cmv hmmcv hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.			114		cmv		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2
cmsearch_deoverlap	0.08+galaxy2	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	Biology Medicine	Comparison Alignment	2982	cmsearch-deoverlap	perl		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
blockclust	1.1.1	blockclust	BlockClust detects transcripts with similar processing patterns.			2288		blockclust		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
aresite2	0.1.2	AREsite2_REST	AREsite2 REST Interface			76		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
antarna	1.1	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .			306		antarna		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
pubchem_rest_tool	0.1.0	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.			0				To update
replace_column_by_key_value_file	0.2	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.			626596				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
repeat_masker	0.1.2	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.			21398		RepeatMasker		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
racon	1.5.0	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Whole genome sequencing Sequence assembly	Genome assembly Mapping assembly	53784	Racon	racon		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
qiime2_dbotu_q2	2022.11.1+galaxy0	qiime2_dbotu_q2	q2-dbotu is a Qiime 2 plugin for performing OTU clustering	Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	0	qiime2			To update	UseGalaxy.eu1
proteomics_improviser	1.1.0.1	proteomics_improviser	Visualisation of PepXML files			0				To update
protein_properties	0.2.0	bg_protein_properties	Calculation of various properties from given protein sequences			684		biopython		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
protease_prediction	0.9	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.			160		eden		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
plotly_regression_performance_plots	0.1	plotly_regression_performance_plots	performance plots for regression problems			1698		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
plotly_parallel_coordinates_plot	0.2	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly			2002		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
plotly_ml_performance_plots	0.4	plotly_ml_performance_plots	performance plots for machine learning problems			3661		galaxy-ml		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
platypus	0.0.11	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data			0		platypus		To update
piranha	1.2.1.0	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data			2094		piranha		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
pharmcat		pharmcat	Pharmacogenomics Clinical Annotation Tool			432				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
pgtools		pg_dump pg_import pg_query	tool suite for dealing with Postgresql databases from Galaxy's history			0		postgresql		To update
pfamscan	1.6	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	Sequence analysis	Protein sequence analysis	2047	pfamscan	pfam_scan		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
stats_perf_tool	5.11.0	stats_perf_tool	suitable for boolean classification problems			0		perf		To update
peakachu	0.2.0+galaxy1	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data			3490		peakachu		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
pandas_rolling_window	0.1	pandas_rolling_window	Rolling window calculations			350		numpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
openms	2.1.0	AccurateMassSearch AdditiveSeries BaselineFilter CVInspector CompNovo CompNovoCID ConsensusID ConsensusMapNormalizer ConvertTSVToTraML ConvertTraMLToTSV DTAExtractor DeMeanderize Decharger DecoyDatabase Digestor DigestorMotif EICExtractor ERPairFinder ExternalCalibration FFEval FalseDiscoveryRate FeatureFinderCentroided FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMRM FeatureFinderMetabo FeatureFinderMultiplex FeatureFinderSuperHirn FeatureLinkerLabeled FeatureLinkerUnlabeled FeatureLinkerUnlabeledQT FidoAdapter FileConverter FileFilter FileInfo FileMerger FuzzyDiff HighResPrecursorMassCorrector IDConflictResolver IDDecoyProbability IDExtractor IDFileConverter IDFilter IDMapper IDMassAccuracy IDMerger IDPosteriorErrorProbability IDRTCalibration IDRipper IDScoreSwitcher IDSplitter ITRAQAnalyzer InclusionExclusionListCreator InspectAdapter InternalCalibration IsobaricAnalyzer LabeledEval LowMemPeakPickerHiRes LowMemPeakPickerHiRes_RandomAccess LuciphorAdapter MRMMapper MRMPairFinder MRMTransitionGroupPicker MSGFPlusAdapter MSSimulator MapAlignmentEvaluation MapNormalizer MapRTTransformer MapStatistics MascotAdapter MascotAdapterOnline MassCalculator MassTraceExtractor MetaProSIP MetaboliteSpectralMatcher MultiplexResolver MzMLSplitter MzTabExporter NoiseFilterGaussian NoiseFilterSGolay OpenSwathAnalyzer OpenSwathAssayGenerator OpenSwathChromatogramExtractor OpenSwathConfidenceScoring OpenSwathDIAPreScoring OpenSwathDecoyGenerator OpenSwathFeatureXMLToTSV OpenSwathFileSplitter OpenSwathMzMLFileCacher OpenSwathRTNormalizer OpenSwathRewriteToFeatureXML OpenSwathWorkflow PTModel PTPredict PeakPickerHiRes PeakPickerIterative PeakPickerWavelet PepNovoAdapter PeptideIndexer PhosphoScoring PrecursorIonSelector PrecursorMassCorrector ProteinInference ProteinQuantifier ProteinResolver QCCalculator QCEmbedder QCExporter QCExtractor QCImporter QCMerger QCShrinker RNPxl RNPxlXICFilter RTEvaluation RTModel RTPredict SemanticValidator SequenceCoverageCalculator SimpleSearchEngine SpecLibCreator SpectraFilterBernNorm SpectraFilterMarkerMower SpectraFilterNLargest SpectraFilterNormalizer SpectraFilterParentPeakMower SpectraFilterScaler SpectraFilterSqrtMower SpectraFilterThresholdMower SpectraFilterWindowMower SpectraMerger SvmTheoreticalSpectrumGeneratorTrainer TICCalculator TMTAnalyzer TOFCalibration TextExporter TopPerc TransformationEvaluation XMLValidator XTandemAdapter	OpenMS in version 2.1.			114319		openms		To update	UseGalaxy.be19 UseGalaxy.cz135 UseGalaxy.eu135 UseGalaxy.no134 UseGalaxy.or34
numeric_clustering	0.9	numeric_clustering	Clustering tool for numberic values			488		anaconda		To update	UseGalaxy.fr1
nucleosome_prediction	3.0	Nucleosome	Prediction of Nucleosomes Positions on the Genome	Structural genomics Nucleic acid sites, features and motifs	Prediction and recognition Nucleosome position prediction Sequence analysis	865	nucleosome_prediction	nucleosome_prediction		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
nextdenovo	2.5.0	nextdenovo	String graph-based de novo assembler for long reads	Sequencing Sequence assembly	De-novo assembly Genome assembly	543	nextdenovo	nextdenovo		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
netboxr	1.6.0	netboxr	netboxr enables automated discovery of biological process modules by network analysis			13		bioconductor-netboxr		To update	UseGalaxy.cz1 UseGalaxy.eu1
nanopolish	0.14.0	nanopolish_eventalign nanopolish_methylation nanopolish_polya nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.			12419		nanopolish		Up-to-date	UseGalaxy.be4 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4 UseGalaxy.or4
music	0.1.1	music_construct_eset music_inspect_eset music_manipulate_eset music_compare music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)			6251	music_deconvolution	music-deconvolution		Up-to-date	UseGalaxy.cz5 UseGalaxy.eu5 UseGalaxy.or5
motus	3.1.0	mereg_mOTUs_tables motus_profiler	Tool for profiling the abundance of microbial taxa.	Metagenomics	Taxonomic classification	76	mOTUs	motus		Up-to-date	UseGalaxy.eu2 UseGalaxy.fr2
molecule_to_gspan	0.2	bg_mol2gspan	converter			0		openbabel		To update
mitohifi	3.2.3	mitohifi	Assembly mitogenomes from Pacbio HiFi read.			2551				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
minipolish	0.2.0	minipolish	Polishing miniasm assemblies	Sequence assembly Sequencing	Localised reassembly Read depth analysis	251	minipolish	minipolish		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
minced	0.2.0	minced	MinCED - Mining CRISPRs in Environmental Datasets			1972		minced		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
miclip	1.2.0	mi_clip	Identification of binding sites in CLIP-Seq data.			0		Rscript		To update
mgnify_seqprep	1.2	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	Genomics Sequence assembly Sequencing Probes and primers	Nucleic acid design	1254	seqprep			To update	UseGalaxy.or1
metilene	0.2.6.1	metilene	Differential DNA methylation calling			5981		metilene		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
methylkit	0.99.2	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.			7		bioconductor-methylkit		To update	UseGalaxy.fr1
pileometh	0.5.2	pileometh	A tool for processing bisulfite sequencing alignments			28578		methyldackel		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
methtools	0.1.1	methtools_calling r_correlation_matrix methtools_destrand methtools_dmr methtools_filter methtools_plot smooth_running_window methtools_tiling	tools for methylation analysis			5461		methtools		To update
mavedb_importer	0.9	mavedb_importer	data source for MaveDB			10				To update	UseGalaxy.eu1
markitdown	0.1.1	markitdown	Convert documents to Markdown using markitdown			0				To update	UseGalaxy.eu1
mafft	7.526	rbc_mafft_add rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	Sequence analysis	Multiple sequence alignment	345522	MAFFT	mafft		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
llm_hub	1.101.0	llm_hub	LiteLLM - Call all LLM APIs using the OpenAI format.			0		python		To update	UseGalaxy.eu1
lighter	1.0	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	Sequencing Whole genome sequencing DNA Genomics	k-mer counting Sequence read processing Sequencing quality control Sequencing error detection	180	lighter	lighter		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
labels	1.0.5.0	bg_labels	remaps and annotates alignments			0		labels		To update
run_jupyter_job	0.0.1	run_jupyter_job	Run jupyter notebook script in Galaxy			33				To update
jbrowse2	2.17.0	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	Mapping Structural variation Genomics Gene structure Sequence assembly	Genome visualisation Structure visualisation Pathway visualisation	2924	jbrowse_2	jbrowse2		To update	UseGalaxy.eu1 UseGalaxy.or1
itsx	1.1.3	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	Functional, regulatory and non-coding RNA Microbiology	Sequence feature detection	2235	ITSx	itsx		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
iprscan5			Interproscan queries the interpro database and provides annotations.			0				To update
instagraal	0.1.6	instagraal	Large genome reassembly based on Hi-C data	Sequence assembly Mapping Metagenomics Statistics and probability DNA binding sites	Genome assembly Mapping assembly Genetic mapping Scaffolding	159	instagraal			To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
yolo	8.3.0	json2yolosegment yolo_predict yolo_training	tools for building yolo workflows.			0				To update	UseGalaxy.eu3
Wound healing scratch assay image analysis	1.6.1	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays			31		fiji-morpholibj		Up-to-date	UseGalaxy.eu1
imagemagick	7.1.2-2	imagemagick_image_compare imagemagick_image_convert imagemagick_image_montage	Contains tools based on ImageMagick			0		imagemagick		To update	UseGalaxy.or3
imagej2	20240614	imagej2_adjust_threshold_binary imagej2_analyze_particles_binary imagej2_analyze_skeleton imagej2_binary_to_edm imagej2_bunwarpj_adapt_transform imagej2_bunwarpj_align imagej2_bunwarpj_compare_elastic imagej2_bunwarpj_compare_elastic_raw imagej2_bunwarpj_compare_raw imagej2_bunwarpj_compose_elastic imagej2_bunwarpj_compose_raw imagej2_bunwarpj_compose_raw_elastic imagej2_bunwarpj_convert_to_raw imagej2_bunwarpj_elastic_transform imagej2_bunwarpj_raw_transform imagej2_create_image imagej2_crop imagej2_enhance_contrast imagej2_filter imagej2_find_edges imagej2_find_maxima imagej2_make_binary imagej2_math imagej2_noise imagej2_shadows imagej2_sharpen imagej2_skeletonize3d imagej2_smooth imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	Imaging	Image analysis Image annotation Visualisation	1768	imagej		imagej2	To update	UseGalaxy.cz27 UseGalaxy.eu27 UseGalaxy.no27
graphicsmagick	1.3.45	graphicsmagick_image_compare graphicsmagick_image_convert graphicsmagick_image_montage	Contains tools based on GraphicsMagick			2806		graphicsmagick		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu3 UseGalaxy.no2 UseGalaxy.or1
bia_download	0.2.0	bia_download	Tool to query ftp links for study from bioimage archive			13		wget		To update	UseGalaxy.eu1
illumina_methylation_analyser	0.1	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays			0		Rscript		To update
homer			Software for motif discovery and next generation sequencing analysis.			0				To update
hicup	0.9.2	hicup2juicer hicup_deduplicator hicup_digester hicup_filter hicup_hicup hicup_mapper hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.			1786				To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.no6 UseGalaxy.or7
hictk	2.0.2	hictk	Convert cooler to juicebox_hic			51		hictk		To update	UseGalaxy.eu1
hclust2	0.99	hclust2	Plots heatmaps			0		hclust2		To update
graphmap	0.5.2	graphmap_align graphmap_overlap	Mapper for long, error-prone reads.	Gene transcripts RNA-Seq RNA splicing	Sequence trimming EST assembly Read mapping	7528	graphmap	graphmap		To update	UseGalaxy.be2 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2
graphclust	0.1	graphclust	GraphClust can be used for structural clustering of RNA sequences.			6		GraphClust		To update
graph_converter	0.1.0	graph_converter	Convert between different graph formats			0				To update
gotohscan	1.3.0	rbc_gotohscan	Find subsequences in db			72		gotohscan		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
glimmer_hmm			GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)			0				To update
gfastats	1.3.11	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	Computational biology	Data handling	26115	gfastats	gfastats		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
format_metaphlan2_output	0.2.0	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	Taxonomy Metagenomics	Formatting	6878	format_metaphlan2_output			To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
format_cd_hit_output	1.0.0+galaxy1	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file			244				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
footprint	1.0.0	footprint	Find transcription factor footprints			57		footprint		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
flye	2.9.6	flye	Assembly of long and error-prone reads.	Sequence assembly Metagenomics Whole genome sequencing Genomics	Genome assembly De-novo assembly Mapping assembly Cross-assembly	76300	Flye	flye		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
black_forest_labs_flux	2024	black_forest_labs_flux	Using the black forest labs FLUX.1 models to generate image based on user input.			99				To update	UseGalaxy.eu1
flexynesis	0.2.20	flexynesis flexynesis_cbioportal_import flexynesis_plot flexynesis_utils	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.			13		flexynesis		To update	UseGalaxy.eu4
find_subsequences	0.3	bg_find_subsequences				4400		biopython		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
unique	0.4	bg_uniq	This tool returns all unique lines from a tab-separated file.			9247		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
ffmpeg	0.1.0	ffmpeg_converter	A complete, cross-platform solution to record, convert and stream audio and video.			0		ffmpeg		To update	UseGalaxy.eu1
fastq_info	0.25.1	fastq_info	FASTQ info allows to validate single or paired fastq files			23549		fastq_utils		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
epicseg	@VERSION_STRING@	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.			255		epicseg		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
edta		edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.	Workflows Mobile genetic elements Plant biology Transcription factors and regulatory sites Model organisms	De-novo assembly Deisotoping Genome annotation	4601	edta	edta		To update	UseGalaxy.cz1 UseGalaxy.eu1
erga_ear	24.10.15	make_ear	A tool to compile assembly reports and stastics from assembly pipeline			83		reportlab		To update	UseGalaxy.eu1
diffbind			Diffbind provides functions for processing ChIP-Seq data.			0				To update
diff	3.10	diff	GNU diff tool that calculates the differences between two files.			441		diffutils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
crispr_recognition_tool	1.2.0	crispr_recognition_tool	CRISPR Recognition Tool			4491		crisper_recognition_tool		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
cpat	3.0.5	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.			699		cpat		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
compare_humann2_output	0.2.0	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	Metagenomics Gene and protein families	Comparison	332	compare_humann2_outputs			To update	UseGalaxy.cz1 UseGalaxy.no1
combine_metaphlan2_humann2	0.3.0	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	Metagenomics Molecular interactions, pathways and networks	Aggregation	643	combine_metaphlan_and_humann	python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
cleanlab	2.7.1	cleanlab_issue_handler	CleanLab is a package to find various types of issues in a dataset.			0		cleanlab		To update	UseGalaxy.eu1
circexplorer	1.1.9.0	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)			526		circexplorer		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
chipseeker	1.32.0	chipseeker	A tool for ChIP peak annotation and visualization			63025		bioconductor-chipseeker		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
chatgpt_openai_api	2024	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.			546		python		To update	UseGalaxy.eu1
cellprofiler4	4.2.8	cp_cellprofiler4	cellProfiler4 wrapper			55				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
cellprofiler		cp_cellprofiler cp_color_to_gray cp_convert_objects_to_image cp_display_data_on_image cp_enhance_or_suppress_features cp_export_to_spreadsheet cp_gray_to_color cp_identify_primary_objects cp_image_math cp_mask_image cp_measure_granularity cp_measure_image_area_occupied cp_measure_image_intensity cp_measure_image_quality cp_measure_object_intensity cp_measure_object_size_shape cp_measure_texture cp_overlay_outlines cp_relate_objects cp_save_images cp_common cp_tile cp_track_objects	cellProfiler wrapper	Imaging Microarray experiment Genotype and phenotype	Quantification Image analysis Parsing	11862	CellProfiler		cellprofiler	To update	UseGalaxy.be19 UseGalaxy.cz23 UseGalaxy.eu23 UseGalaxy.fr19 UseGalaxy.no19 UseGalaxy.or23
cellpose	3.1.0	cellpose	Cellpose is an anatomical segmentation algorithm			22				To update	UseGalaxy.eu1 UseGalaxy.or1
canu	2.3	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	Genomics	De-novo assembly	19904	canu	canu		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
blockbuster	0.1.2	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.			3384		blockbuster		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
blobtoolkit	4.0.7	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.	Sequence assembly Model organisms Workflows Phylogenomics Zoology Biodiversity	Genome assembly Scaffolding Visualisation Data deposition Data parsing	2663	BlobToolKit			To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
bismark	0.22.1	bismark_pretty_report bismark_bowtie2 bismark_deduplicate bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states			17626		bismark		To update	UseGalaxy.be4 UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.no4 UseGalaxy.or4
bionano	3.7.0	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data			1435				To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
biomodels	1.1	biomodels_biomd0000001066 biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.			113				To update	UseGalaxy.eu2
bioimage_inference	2.4.1	bioimage_inference	Load model from BioImage.IO and make inferences	Machine learning Computer science		59	pytorch	python	pytorch	To update	UseGalaxy.be1 UseGalaxy.eu1 UseGalaxy.or1
bigwig_to_bedgraph	0.1.0	bigwig_to_bedgraph	Convert from bigWig to bedGraph format			7955		ucsc_tools		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
barcode_collapse	0.1.0	barcode_collapse	Paired End randomer aware duplicate removal algorithm			0		pysam		To update
bamhash	1.1	bamhash	Hash BAM and FASTQ files to verify data integrity			188		bamhash		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
atactk_trim_adapters	0.1.6	atactk_trim_adapters	Trim adapters from paired-end HTS reads.			291		atactk		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
antismash	6.1.1	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	Molecular interactions, pathways and networks Gene and protein families	Sequence clustering Gene prediction Differential gene expression analysis	40761	antismash	antismash		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
agat	1.4.0	agat	GTF/GFF analysis toolkit	Genomics	Data handling Genome annotation	6371	agat	agat		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
structure_to_gspan	0.4	structure_to_gspan	Convert RNA structure to GSPAN graphs			3074		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_preprocessing	0.5	preproc	Preprocessing input for GraphClust			1921		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_prepocessing_for_mlocarna	0.4	preMloc	This tool prepares files for locarna step.			2140		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_motif_finder_plot	0.4	motifFinderPlot	Plotting results for GraphClust			71		seaborn		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_nspdk	9.2.3.1	NSPDK_candidateClust nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.			62905		graphclust-wrappers		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.no2
graphclust_mlocarna	0.4	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.			50825		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_fasta_to_gspan	0.4	gspan	Second step of GraphClust			161		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_postprocessing_no_align	0.5	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.			108		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_postprocessing	0.5	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.			2131		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_cmfinder	0.4	cmFinder	Determines consensus motives for sequences.			50693		graphclust-wrappers		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
graphclust_align_cluster	0.1	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.			3101		graphclust-wrappers		To update	UseGalaxy.eu1 UseGalaxy.no1
graphclust_aggregate_alignments	0.6.0	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.			120		graphclust-wrappers		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
10x_bamtofastq	1.4.1	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ			367		10x_bamtofastq		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.or1
vcftools_subset	0.1	vcftools_subset	Select samples from a VCF dataset			286		tabix		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
vcftools_slice	0.1	vcftools_slice	Subset VCF dataset by genomic regions			8748		echo		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
vcftools_merge	0.1.11	vcftools_merge	Merge multiple VCF datasets into a single dataset			1738		tabix		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
vcftools_isec	0.1.1	vcftools_isec	Intersect multiple VCF datasets			1071		tabix		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
vcftools_consensus	0.1.11	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence			0		samtools		To update
vcftools_compare	0.1	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics			653		tabix		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
vcftools_annotate	0.1	vcftools_annotate	Annotate VCF using custom/user-defined annotations			4583		echo		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
t2t_report	1.0.0	t2t_report	Summarize taxonomy			8154		taxonomy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
t2ps	1.0.0	Draw_phylogram	Draw phylogeny	Phylogenomics	Phylogenetic tree visualisation	8430	t2ps	taxonomy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
poisson2test	1.0.0	poisson2test	Poisson two-sample test			1072		taxonomy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
lca_wrapper	1.0.1	lca1	Find lowest diagnostic rank			6273		taxonomy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
kraken2tax	1.2+galaxy0	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.			68046		gawk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
gi2taxonomy	1.1.1	Fetch Taxonomic Ranks	Fetch taxonomic representation	Taxonomy	Database search ID mapping	14747	gi2taxonomy	taxonomy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
find_diag_hits	1.0.0	find_diag_hits	Find diagnostic hits			1857		taxonomy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
snpfreq	1.0.1	hgv_snpFreq	snpFreq significant SNPs in case-control data			980		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
hgv_hilbertvis	1.0.0	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve			265		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
hgv_fundo	1.0.0	hgv_funDo	FunDO human genes associated with disease terms			1794				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tables_arithmetic_operations	1.0.0	tables_arithmetic_operations	Arithmetic Operations on tables			2310		perl		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
subtract_query	0.1	subtract_query1	Subtract Whole Dataset from another dataset			43295		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
subtract	1.0.0	gops_subtract_1	Subtract the intervals of two datasets			775082		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
merge	1.0.0	gops_merge_1	Merge the overlapping intervals of a dataset			697093		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
join	1.0.0	gops_join_1	Join the intervals of two datasets side-by-side			848340		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
intersect	1.0.0	gops_intersect_1	Intersect the intervals of two datasets			1142164		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
get_flanks	1.0.0	get_flanks1	Get flanks returns flanking region/s for every gene			568957		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
flanking_features	4.0.1	flanking_features_1	Fetch closest non-overlapping feature for every interval			35163		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
coverage	1.0.0	gops_coverage_1	Coverage of a set of intervals on second set of intervals			46481		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
concat	1.0.1	gops_concat_1	Concatenate two bed files			683959		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
complement	1.0.0	gops_complement_1	Complement intervals of a dataset			5536		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
cluster	1.0.0	gops_cluster_1	Cluster the intervals of a dataset			32992		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
basecoverage	1.0.0	gops_basecoverage_1	Base Coverage of all intervals			46501		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
xy_plot	1.0.2	XY_Plot_1	Plotting tool for multiple series and graph types			25190		r-base		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
windowsplitter	1.0.1	winSplitter	Make windows			3974		bx-python		To update	UseGalaxy.or1
weightedaverage	1.0.1	wtavg	Assign weighted-average of the values of features overlapping an interval			2308		galaxy-ops		To update	UseGalaxy.or1
vcf_intersect	1.0.0	vcf_intersect	Generate the intersection of two VCF files			482				To update
vcf_filter	1.0.0	vcf_filter	Filter a VCF file			1146				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
vcf_extract	1.0.0	vcf_extract	Extract reads from a specified region			569				To update
vcf_annotate	1.0.0	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)			342				To update
vcf2pgsnp	1.0.0	vcf2pgSnp	VCF to pgSnp			2966				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
varscan_version_2	2.4.2	varscan	VarScan wrapper			66251		varscan		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
ucsc_custom_track	1.0.1	build_ucsc_custom_track_1	Build custom track for UCSC genome browser			19391		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
trimmer	0.0.1	trimmer	Trim leading or trailing characters.			118310				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
tophat_fusion_post	0.1	tophat_fusion_post	Wrapper for Tophat-Fusion post step			1183		blast+		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tophat2	2.1.1	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads			388052		bowtie2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tophat	1.5.0	tophat	Tophat for Illumina			66525		samtools		To update
tabular_to_fasta	1.1.1	tab2fasta	Tabular-to-FASTA			627706		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
table_annovar	0.2	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered			64533		annovar		To update
t_test_two_samples	1.0.1	t_test_two_samples	T Test for Two Samples			2659		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
substitutions	1.0.1	substitutions1	Fetch substitutions from pairwise alignments			901		bx-python		To update	UseGalaxy.or1
substitution_rates	1.0.0	subRate1	Estimate substitution rates for non-coding regions			4015				To update
split_paired_reads	1.0.0	split_paired_reads	Split paired end reads			397				To update
sicer	1.1	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions			10212		SICER		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
show_tail	1.0.0	Show tail1	Select lines from the end of a file.			28184				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
show_beginning	1.0.0	Show beginning1	Select lines from the beginning of a file.			181555				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
short_reads_trim_seq	1.0.0	trim_reads	Select high quality segments			6877				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
short_reads_figure_score	1.0.2	quality_score_distribution	Build base quality distribution			3523		fontconfig		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
short_reads_figure_high_quality_length	1.0.0	hist_high_quality_score	Histogram of high quality score reads			0		rpy		To update
scatterplot	1.0.3	scatterplot_rpy	Scatterplot of two numeric columns			11290		numpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
sam_bitwise_flag_filter	1.0.1	sam_bw_filter	Filter SAM on bitwise flag values			76717		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
sam2interval	1.0.2	sam2interval	Convert SAM to interval.			20365		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
rmapq	1.0.0	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores			0		rmap		To update
rmap	1.0.0	rmap_wrapper	RMAP for Solexa Short Reads Alignment			0		rmap		To update
remove_beginning	1.0.0	Remove beginning1	Remove lines from the beginning of a file.			353254				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
rcve	1.0.0	rcve1	Compute RCVE			193		R		To update	UseGalaxy.or1
quality_filter	1.0.1	qualityFilter	Filter nucleotides based on quality scores			724		bx-python		To update
principal_component_analysis	1.0.2	pca1	Principal Component Analysis			18278		rpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
plot_from_lda	1.0.1	plot_for_lda_output1	Draw ROC plot on "Perform LDA" output			1138		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
pileup_parser	1.0.2	pileup_parser	Filter pileup on coverage and SNPs			59527		perl		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
pileup_interval	1.0.3	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases			9393		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
pgsnp2gd_snp	1.0.0	pgSnp2gd_snp	Convert from pgSnp to gd_snp			0				To update
pearson_correlation	1.0.0	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns			2				To update
partialr_square	1.0.0	partialRsq	Compute partial R square			142		R		To update	UseGalaxy.or1
mutate_snp_codon	1.0.0	mutate_snp_codon_1	Mutate Codons with SNPs			472				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
multispecies_orthologous_microsats	1.0.0	multispecies_orthologous_microsats	Extract orthologous microsatellites			0		bx-sputnik		To update
mine	0.0.1	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration			75		MINE		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
microsats_mutability	1.1.0	microsats_mutability1	Estimate microsatellite mutability by specified attributes			315		bx-python		To update	UseGalaxy.or1
microsats_alignment_level	1.0.0	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments			978		sputnik		To update	UseGalaxy.or1
microsatellite_birthdeath	1.0.0	microsatellite_birthdeath	Identify microsatellite births and deaths			0				To update
merge_cols	1.0.3	mergeCols1	Merge columns together.			171104		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
megablast_xml_parser	1.0.1	megablast_xml_parser	Parse blast XML output			4377		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
mapping_to_ucsc	1.0.0	mapToUCSC	Format mapping data as UCSC custom track			0				To update
maf_cpg_filter	1.0.0	cpgFilter	Mask CpG/non-CpG sites from MAF file			356		bx-python		To update	UseGalaxy.or1
logistic_regression_vif	1.0.1	LogisticRegression	Perform Logistic Regression with vif			173		numpy		To update
linear_regression	1.0.1	LinearRegression1	Perform Linear Regression			1131		R		To update	UseGalaxy.or1
lda_analysis	1.0.1	lda_analy1	Perform Linear Discriminant Analysis			1755		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
lastz_paired_reads	1.1.1	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads			19		lastz		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
kernel_principal_component_analysis	1.0.0	kpca1	Kernel Principal Component Analysis			883		rpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
kernel_canonical_correlation_analysis	1.0.0	kcca1	Kernel Canonical Correlation Analysis			422		rpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
indels_3way	1.0.3	indels_3way	Fetch Indels from 3-way alignments			314				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
histogram	1.0.5	histogram_rpy	Histogram of a numeric column			55379		rpy2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
hisat	1.0.3	hisat	HISAT is a fast and sensitive spliced alignment program.			228		hisat		To update
gmaj	2.0.1	gmaj_1	GMAJ Multiple Alignment Viewer			1008				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
getindels_2way	1.0.0	getIndels_2way	Fetch Indels from pairwise alignments			237		numpy		To update	UseGalaxy.or1
getindelrates_3way	1.0.0	indelRates_3way	Estimate Indel Rates for 3-way alignments			291		bx-python		To update	UseGalaxy.or1
generate_pc_lda_matrix	1.0.0	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA			1419				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
filter_transcripts_via_tracking	0.1	filter_combined_via_tracking	Filter Combined Transcripts			664				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
featurecounter	2.0.0	featureCoverage1	Feature coverage			36100		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
fastqsolexa_to_fasta_qual	1.0.0	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data			8				To update
fastq_trimmer_by_quality	1.1.5	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window			111169		galaxy_sequence_utils		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_to_tabular	1.1.1	fasta2tab	FASTA-to-Tabular converter			330253		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_filter_by_length	1.2	fasta_filter_by_length	Filter sequences by length			172303		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_concatenate_by_species	0.0.1	fasta_concatenate0	Concatenate FASTA alignment by species			63569		bx-python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
fasta_compute_length	1.0.4	fasta_compute_length	Compute sequence length			69533		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
express	1.1.1	express	Quantify the abundances of a set of target sequences from sampled subsequences			4425		eXpress		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
dwt_var_perfeature	1.0.2	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms			290		r-bitops		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
dwt_var_perclass	1.0.1	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences			153		r-waveslim		To update	UseGalaxy.or1
dwt_ivc_all	1.0.1	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences			144		r-waveslim		To update	UseGalaxy.or1
dwt_cor_avb_all	1.0.1	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features			145		r-waveslim		To update	UseGalaxy.or1
dwt_cor_ava_perclass	1.0.1	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences			162		r-waveslim		To update	UseGalaxy.or1
draw_stacked_barplots	1.0.0	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria			469		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
divide_pg_snp	1.0.0	dividePgSnp	Separate pgSnp alleles into columns			212				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
dgidb_annotator	0.1	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)			373				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
delete_overlapping_indels	1.0.0	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file			40				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
cut_columns	1.0.2	Cut1	Select columns from a dataset.			3047543				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
cummerbund_to_tabular	1.0.1	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.			3899				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
cummerbund	2.16.0	cummeRbund	Wrapper for the Bioconductor cummeRbund library			20572		fonts-conda-ecosystem		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
ctd_batch	1.0.0	ctdBatch_1	CTD analysis of chemicals, diseases, or genes			666				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
count_gff_features	0.2	count_gff_features	Count GFF Features			2351		galaxy-ops		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
correlation	1.0.0	cor2	Correlation for numeric columns			6747		rpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
convert_solid_color2nuc	1.0.0	color2nuc	Convert Color Space to Nucleotides			0				To update
convert_characters	1.0.1	Convert characters1	Convert delimiters to tab.			204876		python		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
condense_characters	1.0.0	Condense characters1	Condense consecutive characters.			2413				To update	UseGalaxy.or1
compute_q_values	1.0.1	compute_q_values	Compute q-values based on multiple simultaneous tests p-values			35		R		To update
compute_motifs_frequency	1.0.0	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.			442				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
compute_motif_frequencies_for_all_motifs	1.0.0	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.			474				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
change_case	1.0.1	ChangeCase	Convert column case.			33846		perl		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
cd_hit_dup	0.0.1	cd_hit_dup	simple tool for removing duplicates from sequencing reads			7789		cd-hit-auxtools		To update	UseGalaxy.or1
ccat	0.0.2	peakcalling_ccat	Control-based ChIP-seq Analysis Tool			179		ccat		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
categorize_elements_satisfying_criteria	1.0.0	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.			249				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
canonical_correlation_analysis	1.0.0	cca1	Canonical Correlation Analysis			582		R		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
bowtie_wrappers	1.2.0	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.			248551		bowtie		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
blat_mapping	1.0.0	blat2wig	Coverage of the Reads in wiggle format			0				To update
blat_coverage_report	1.0.0	generate_coverage_report	Polymorphism of the Reads			0				To update
best_regression_subsets	1.0.0	BestSubsetsRegression1	Perform Best-subsets Regression			260		numpy		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
add_value	1.0.1	addValue	Add a value as a new column.			689289		perl		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
suite_qiime2_core						0				To update
qiime2	2025.7.0+dist.h44bd78f6	qiime2_core__tools__export qiime2_core__tools__import qiime2_core__tools__import_fastq		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	95748	qiime2			To update	UseGalaxy.cz2 UseGalaxy.eu3 UseGalaxy.fr2 UseGalaxy.or2
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__vsearch__cluster_features_closed_reference qiime2__vsearch__cluster_features_de_novo qiime2__vsearch__cluster_features_open_reference qiime2__vsearch__dereplicate_sequences qiime2__vsearch__fastq_stats qiime2__vsearch__merge_pairs qiime2__vsearch__uchime_denovo qiime2__vsearch__uchime_ref		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	451	qiime2			To update	UseGalaxy.cz8 UseGalaxy.eu8 UseGalaxy.fr7 UseGalaxy.or8
qiime2	0.0.1.dev0+q2galaxy.2025.7.0	qiime2__vizard__boxplot qiime2__vizard__heatmap qiime2__vizard__lineplot qiime2__vizard__scatterplot_2d		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	3	qiime2			To update	UseGalaxy.eu1
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__taxa__barplot qiime2__taxa__collapse qiime2__taxa__filter_seqs qiime2__taxa__filter_table		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	2528	qiime2			To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.or4
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__stats__alpha_group_significance qiime2__stats__collate_stats qiime2__stats__facet_across qiime2__stats__facet_within qiime2__stats__mann_whitney_u qiime2__stats__mann_whitney_u_facet qiime2__stats__plot_rainclouds qiime2__stats__prep_alpha_distribution qiime2__stats__wilcoxon_srt qiime2__stats__wilcoxon_srt_facet		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	0	qiime2			To update	UseGalaxy.eu6
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__sample_classifier__classify_samples qiime2__sample_classifier__classify_samples_from_dist qiime2__sample_classifier__classify_samples_ncv qiime2__sample_classifier__confusion_matrix qiime2__sample_classifier__fit_classifier qiime2__sample_classifier__fit_regressor qiime2__sample_classifier__heatmap qiime2__sample_classifier__metatable qiime2__sample_classifier__predict_classification qiime2__sample_classifier__predict_regression qiime2__sample_classifier__regress_samples qiime2__sample_classifier__regress_samples_ncv qiime2__sample_classifier__scatterplot qiime2__sample_classifier__split_table qiime2__sample_classifier__summarize		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	64	qiime2			To update	UseGalaxy.cz15 UseGalaxy.eu15 UseGalaxy.fr15 UseGalaxy.or15
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__rescript__cull_seqs qiime2__rescript__degap_seqs qiime2__rescript__dereplicate qiime2__rescript__edit_taxonomy qiime2__rescript__evaluate_classifications qiime2__rescript__evaluate_cross_validate qiime2__rescript__evaluate_fit_classifier qiime2__rescript__evaluate_seqs qiime2__rescript__evaluate_taxonomy qiime2__rescript__extract_seq_segments qiime2__rescript__filter_seqs_length qiime2__rescript__filter_seqs_length_by_taxon qiime2__rescript__filter_taxa qiime2__rescript__get_bv_brc_genome_features qiime2__rescript__get_bv_brc_genomes qiime2__rescript__get_bv_brc_metadata qiime2__rescript__get_gtdb_data qiime2__rescript__get_midori2_data qiime2__rescript__get_ncbi_data qiime2__rescript__get_ncbi_data_protein qiime2__rescript__get_ncbi_genomes qiime2__rescript__get_pr2_data qiime2__rescript__get_silva_data qiime2__rescript__get_unite_data qiime2__rescript__merge_taxa qiime2__rescript__orient_reads qiime2__rescript__orient_seqs qiime2__rescript__parse_silva_taxonomy qiime2__rescript__reverse_transcribe qiime2__rescript__subsample_fasta qiime2__rescript__trim_alignment		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	7	qiime2			To update	UseGalaxy.eu3
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__quality_filter__q_score		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	147	qiime2			To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__quality_control__bowtie2_build qiime2__quality_control__decontam_identify qiime2__quality_control__decontam_identify_batches qiime2__quality_control__decontam_score_viz qiime2__quality_control__evaluate_composition qiime2__quality_control__evaluate_seqs qiime2__quality_control__evaluate_taxonomy qiime2__quality_control__exclude_seqs qiime2__quality_control__filter_reads		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	104	qiime2			To update	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.or6
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__phylogeny__align_to_tree_mafft_fasttree qiime2__phylogeny__align_to_tree_mafft_iqtree qiime2__phylogeny__align_to_tree_mafft_raxml qiime2__phylogeny__fasttree qiime2__phylogeny__filter_table qiime2__phylogeny__filter_tree qiime2__phylogeny__iqtree qiime2__phylogeny__iqtree_ultrafast_bootstrap qiime2__phylogeny__midpoint_root qiime2__phylogeny__raxml qiime2__phylogeny__raxml_rapid_bootstrap qiime2__phylogeny__robinson_foulds		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	1068	qiime2			To update	UseGalaxy.cz12 UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.or12
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__metadata__distance_matrix qiime2__metadata__merge qiime2__metadata__shuffle_groups qiime2__metadata__tabulate		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	2512	qiime2			To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.or3
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__longitudinal__anova qiime2__longitudinal__feature_volatility qiime2__longitudinal__first_differences qiime2__longitudinal__first_distances qiime2__longitudinal__linear_mixed_effects qiime2__longitudinal__maturity_index qiime2__longitudinal__nmit qiime2__longitudinal__pairwise_differences qiime2__longitudinal__pairwise_distances qiime2__longitudinal__plot_feature_volatility qiime2__longitudinal__volatility		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	209	qiime2			To update	UseGalaxy.cz11 UseGalaxy.eu11 UseGalaxy.fr11 UseGalaxy.or11
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__fragment_insertion__classify_otus_experimental qiime2__fragment_insertion__filter_features qiime2__fragment_insertion__sepp		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	104	qiime2			To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.or3
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__feature_table__core_features qiime2__feature_table__filter_features qiime2__feature_table__filter_features_conditionally qiime2__feature_table__filter_samples qiime2__feature_table__filter_seqs qiime2__feature_table__group qiime2__feature_table__heatmap qiime2__feature_table__merge qiime2__feature_table__merge_seqs qiime2__feature_table__merge_taxa qiime2__feature_table__normalize qiime2__feature_table__presence_absence qiime2__feature_table__rarefy qiime2__feature_table__relative_frequency qiime2__feature_table__rename_ids qiime2__feature_table__split qiime2__feature_table__subsample_ids qiime2__feature_table__summarize qiime2__feature_table__summarize_plus qiime2__feature_table__tabulate_feature_frequencies qiime2__feature_table__tabulate_sample_frequencies qiime2__feature_table__tabulate_seqs qiime2__feature_table__transpose		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	5627	qiime2			To update	UseGalaxy.cz17 UseGalaxy.eu17 UseGalaxy.fr17 UseGalaxy.or17
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__feature_classifier__blast qiime2__feature_classifier__classify_consensus_blast qiime2__feature_classifier__classify_consensus_vsearch qiime2__feature_classifier__classify_hybrid_vsearch_sklearn qiime2__feature_classifier__classify_sklearn qiime2__feature_classifier__extract_reads qiime2__feature_classifier__find_consensus_annotation qiime2__feature_classifier__fit_classifier_naive_bayes qiime2__feature_classifier__fit_classifier_sklearn qiime2__feature_classifier__makeblastdb qiime2__feature_classifier__vsearch_global		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	3350	qiime2			To update	UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr10 UseGalaxy.or10
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__emperor__biplot qiime2__emperor__plot qiime2__emperor__procrustes_plot		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	380	qiime2			To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.or3
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__diversity_lib__alpha_passthrough qiime2__diversity_lib__beta_passthrough qiime2__diversity_lib__beta_phylogenetic_meta_passthrough qiime2__diversity_lib__beta_phylogenetic_passthrough qiime2__diversity_lib__bray_curtis qiime2__diversity_lib__faith_pd qiime2__diversity_lib__jaccard qiime2__diversity_lib__observed_features qiime2__diversity_lib__pielou_evenness qiime2__diversity_lib__shannon_entropy qiime2__diversity_lib__unweighted_unifrac qiime2__diversity_lib__weighted_unifrac		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	2095	qiime2			To update	UseGalaxy.cz12 UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.or12
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__diversity__adonis qiime2__diversity__alpha qiime2__diversity__alpha_correlation qiime2__diversity__alpha_group_significance qiime2__diversity__alpha_phylogenetic qiime2__diversity__alpha_rarefaction qiime2__diversity__beta qiime2__diversity__beta_correlation qiime2__diversity__beta_group_significance qiime2__diversity__beta_phylogenetic qiime2__diversity__beta_rarefaction qiime2__diversity__bioenv qiime2__diversity__core_metrics qiime2__diversity__core_metrics_phylogenetic qiime2__diversity__filter_alpha_diversity qiime2__diversity__filter_distance_matrix qiime2__diversity__mantel qiime2__diversity__partial_procrustes qiime2__diversity__pcoa qiime2__diversity__pcoa_biplot qiime2__diversity__procrustes_analysis qiime2__diversity__tsne qiime2__diversity__umap		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	3866	qiime2			To update	UseGalaxy.cz21 UseGalaxy.eu22 UseGalaxy.fr21 UseGalaxy.or21
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__demux__emp_paired qiime2__demux__emp_single qiime2__demux__filter_samples qiime2__demux__partition_samples_paired qiime2__demux__partition_samples_single qiime2__demux__subsample_paired qiime2__demux__subsample_single qiime2__demux__summarize qiime2__demux__tabulate_read_counts		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	2279	qiime2			To update	UseGalaxy.cz6 UseGalaxy.eu6 UseGalaxy.fr6 UseGalaxy.or6
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__deblur__denoise_16S qiime2__deblur__denoise_other qiime2__deblur__visualize_stats		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	337	qiime2			To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.or3
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__dada2__denoise_ccs qiime2__dada2__denoise_paired qiime2__dada2__denoise_pyro qiime2__dada2__denoise_single		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	2540	qiime2			To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.or4
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__cutadapt__demux_paired qiime2__cutadapt__demux_single qiime2__cutadapt__trim_paired qiime2__cutadapt__trim_single		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	570	qiime2			To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr4 UseGalaxy.or4
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__composition__add_pseudocount qiime2__composition__ancom qiime2__composition__ancombc qiime2__composition__ancombc2 qiime2__composition__ancombc2_visualizer qiime2__composition__da_barplot qiime2__composition__tabulate		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	822	qiime2			To update	UseGalaxy.cz4 UseGalaxy.eu4 UseGalaxy.fr2 UseGalaxy.or4
qiime2	2025.7.0+q2galaxy.2025.7.0	qiime2__alignment__mafft qiime2__alignment__mafft_add qiime2__alignment__mask		Microbial ecology Metatranscriptomics Metagenomics	Demultiplexing Visualisation Taxonomic classification	576	qiime2			To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.fr3 UseGalaxy.or3
segalign	0.1.2.7	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.			379		segalign-galaxy		Up-to-date	UseGalaxy.or1
rdeval	0.0.7	rdeval rdeval_report	rdeval is a General purpose, multithreaded read analysis and manipulation tool.			0		rdeval		Up-to-date	UseGalaxy.or2
ncbi_fcs_adaptor	0.5.0	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.			2155				To update	UseGalaxy.or1
ncbi_egapx	0.4.1	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)			515				To update	UseGalaxy.eu1 UseGalaxy.or1
kegalign	0.1.2.7	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.			138		kegalign-full		Up-to-date	UseGalaxy.or1
batched_lastz	1.04.22	batched_lastz	Galaxy wrapper for the batching Lastz runs			226		lastz		To update	UseGalaxy.or1
wsi_extract_top_view	0.2-2	ip_wsi_extract_top_view	WSI Extract Top View			38		scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
voronoi_tesselation	0.22.0	voronoi_tessellation	Compute Voronoi tesselation	Imaging Software engineering Literature and language	Image analysis Image annotation Visualisation Data handling	61	scikit-image	scikit-image	scikit-image	To update	UseGalaxy.eu1
visceral_evaluatesegmentation	0.5-2	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			25		visceral-evaluatesegmentation	evaluatesegmentation-tool	To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
unzip	6.0	unzip	Unzip file			10418		unzip		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
superdsm	0.2.0	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images		Image analysis	26	superdsm	superdsm	superdsm	To update	UseGalaxy.cz1 UseGalaxy.eu1
spot_detection_2d	0.1	ip_spot_detection_2d	Spot detection in 2D image sequence	Imaging Bioinformatics	Image analysis	79	galaxy_image_analysis	giatools		To update	UseGalaxy.cz1 UseGalaxy.eu1
split_labelmap	0.2-3	ip_split_labelmap	Split Labelmaps	Imaging Bioinformatics	Image analysis	51	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
split_image	2.2.3	ip_split_image	Split image along axes			0		numpy		To update	UseGalaxy.eu1
slice_image	0.3-4	ip_slice_image	Slice image	Imaging Bioinformatics	Image analysis	127	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
segmetrics	1.4	ip_segmetrics	Image segmentation and object detection performance measures		Image analysis	10	segmetrics	segmetrics	segmetrics	To update	UseGalaxy.cz1 UseGalaxy.eu1
scale_image	0.18.3	ip_scale_image	Scale image	Imaging Software engineering Literature and language	Image analysis Image annotation Visualisation Data handling	521	scikit-image	scikit-image	scikit-image	To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rfove	2023.11.12	rfove	Perform segmentation region-based fitting of overlapping ellipses	Cell biology Biomedical science Imaging	Image analysis	15	rfove			To update	UseGalaxy.eu1
repeat_channels	1.26.4	repeat_channels	Convert single-channel to multi-channel image	Imaging Bioinformatics	Image analysis	14	galaxy_image_analysis	numpy		To update	UseGalaxy.eu1
projective_transformation_points	0.1.1	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	Imaging Bioinformatics	Image analysis	21445	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
projective_transformation	0.1.2	ip_projective_transformation	Projective transformation	Imaging Bioinformatics	Image analysis	86	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
points_association_nn	0.0.3-2	ip_points_association_nn	Association of points in consecutive frames	Imaging Bioinformatics	Image analysis	46	galaxy_image_analysis	numpy		To update	UseGalaxy.cz1 UseGalaxy.eu1
points2labelimage	0.4.1	ip_points_to_label	Points to label image	Imaging Bioinformatics	Image analysis	54	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
plantseg	1.8.1	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	Plant biology Bioimaging Light microscopy Machine learning Electron microscopy	Network analysis Quantification Microscope image visualisation	0	plantseg	plant-seg		To update	UseGalaxy.eu1
permutate_axis	0.2-2	ip_permutate_axis	Permutates axes	Imaging Bioinformatics	Image analysis	42	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
overlay_images	0.0.4	ip_overlay_images	Overlay two images	Imaging Bioinformatics	Image analysis	340	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
orientationpy	0.2.0.4	orientationpy	Compute image orientation			0		orientationpy	orientationj	Up-to-date	UseGalaxy.eu1
morphological_operations	1.12.0	morphological_operations	Apply morphological operations to images			0		scipy	scipy	To update	UseGalaxy.eu1
mergeneighboursinlabelimage	0.3-2	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	Imaging Bioinformatics	Image analysis	25	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
mahotas_features	0.7-2	ip_mahotas_features	Compute image features using mahotas.			44		mahotas	mahotas-feature-computation	To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
landmark_registration	0.1.0-2	ip_landmark_registration	Landmark Registration	Imaging Bioinformatics	Image analysis	936	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
labelimage2points	0.2-2	ip_labelimage_to_points	Label Image to Points	Imaging Bioinformatics	Image analysis	38	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
label_to_binary	1.26.4	label_to_binary	Convert label map to binary image	Imaging Bioinformatics	Image analysis	0	galaxy_image_analysis	numpy		To update	UseGalaxy.eu1
imagecoordinates_flipaxis	0.1-2	imagecoordinates_flipaxis	Flip coordinate axes	Imaging Bioinformatics	Image analysis	21850	galaxy_image_analysis	pandas		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
image_registration_affine	0.0.3-2	ip_image_registration	Intensity-based Image Registration	Imaging Bioinformatics	Image analysis	16	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1
image_math	1.26.4	image_math	Process images using arithmetic expressions			74		numpy		To update	UseGalaxy.eu1 UseGalaxy.or1
image_info	5.7.1	ip_imageinfo	Extracts image metadata			847		bftools	python-bioformats	To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
detection_viz	0.3-2	ip_detection_viz	Detection Visualization	Imaging Bioinformatics	Image analysis	49	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
curve_fitting	0.0.3-2	ip_curve_fitting	Polynomial curve fitting to data points	Imaging Bioinformatics	Image analysis	29	galaxy_image_analysis	numpy		To update	UseGalaxy.cz1 UseGalaxy.eu1
crop_image	0.4.1	ip_crop_image	Crop image			0	giatools	giatools		Up-to-date	UseGalaxy.eu1
count_objects	0.0.5-2	ip_count_objects	Count Objects	Imaging Bioinformatics	Image analysis	503	galaxy_image_analysis	scikit-image		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
coordinates_of_roi	0.0.4-2	ip_coordinates_of_roi	Coordinates of ROI	Imaging Bioinformatics	Image analysis	16547	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
concat_channels	0.3-1	ip_concat_channels	Concatenate images	Imaging Bioinformatics	Image analysis	84	galaxy_image_analysis	scikit-image		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
colorize_labels	3.2.1	colorize_labels	Colorize label map			62		networkx		To update	UseGalaxy.eu1
color_deconvolution	0.9	ip_color_deconvolution	Color-deconvolution methods	Imaging Bioinformatics	Image analysis	45	galaxy_image_analysis	scikit-image		To update	UseGalaxy.eu1 UseGalaxy.no1
bioformats2raw	0.7.0	bf2raw	Convert image to OME-Zarr			62				To update	UseGalaxy.eu1 UseGalaxy.fr1
binaryimage2points	0.1-2	ip_binaryimage_to_points	Binary Image to Points	Imaging Bioinformatics	Image analysis	29	galaxy_image_analysis	numpy		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
binary2labelimage	0.6	ip_binary_to_labelimage	Binary 2 label image	Imaging Bioinformatics	Image analysis	1689	galaxy_image_analysis	giatools		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
bfconvert	6.7.0	ip_convertimage	Convert image			2118		bftools	python-bioformats	To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
background_removal	0.24.0	background_removal	Background removal filters using scikit-image			30		scikit-image		To update	UseGalaxy.eu1
anisotropic_diffusion	0.4.0	ip_anisotropic_diffusion	Anisotropic image diffusion			41		medpy		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
2d_simple_filter	1.12.0	ip_filter_standard	2d simple filter			6612		scipy	scipy	To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
2d_histogram_equalization	0.18.1	ip_histogram_equalization	2d histogram equalization	Imaging Software engineering Literature and language	Image analysis Image annotation Visualisation Data handling	1071	scikit-image	scikit-image	scikit-image	To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
2d_filter_segmentation_by_features	0.0.1-4	ip_2d_filter_segmentation_by_features	filter segmentation by rules	Imaging Bioinformatics	Image analysis	7015	galaxy_image_analysis	scikit-image		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
2d_feature_extraction	0.18.1	ip_2d_feature_extraction	2D feature extraction	Imaging Software engineering Literature and language	Image analysis Image annotation Visualisation Data handling	14027	scikit-image	scikit-image	scikit-image	To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
2d_auto_threshold	0.25.0	ip_threshold	Automatic thresholding	Imaging Software engineering Literature and language	Image analysis Image annotation Visualisation Data handling	7277	scikit-image	scikit-image	scikit-image	To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
w4mjoinpn	0.98.2	w4mjoinpn	Join positive- and negative-mode W4M datasets			178		coreutils		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
w4mclassfilter	0.98.19	w4mclassfilter	Filter W4M data by values or metadata			4517		r-base		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
w4mcorcov	0.98.18	w4mcorcov	OPLS-DA Contrasts of Univariate Results			386		r-base		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
tripal		analysis_add_analysis analysis_get_analyses analysis_load_blast analysis_load_fasta analysis_load_gff3 analysis_load_go analysis_load_interpro analysis_sync db_index db_populate_mviews entity_publish expression_add_biomaterial expression_add_expression expression_delete_biomaterials expression_get_biomaterials expression_sync_biomaterials feature_delete_orphans feature_sync organism_add_organism organism_get_organisms organism_sync phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal			0		python-tripal		To update
repeatexplorer2	2.3.8	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.			225				To update	UseGalaxy.eu1
jbrowse_to_container		jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container			0		python		To update
genenotebook	0.4.18	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io			295		genoboo		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
chado		analysis_add_analysis analysis_delete_analyses analysis_get_analyses export_export_fasta export_export_gbk export_export_gff3 expression_add_biomaterial expression_add_expression expression_delete_all_biomaterials expression_delete_biomaterials expression_get_biomaterials feature_delete_features feature_get_features feature_load_fasta feature_load_featureprops feature_load_gff feature_load_go load_blast load_interpro organism_add_organism organism_delete_all_organisms organism_delete_organisms organism_get_organisms phylogeny_gene_families phylogeny_gene_order phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado			0		python-chado		To update
askomics		askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/			0		askocli		To update
apollo		create_account feat_from_gff3 create_or_update delete_features delete_organism export fetch_jbrowse iframe list_organism	Access an Apollo instance from Galaxy			4826		apollo		To update	UseGalaxy.cz9 UseGalaxy.eu9 UseGalaxy.no9
msp_split	0.0.2	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data			0				To update
msPurity	1.28.0	mspurity_averagefragspectra mspurity_combineannotations mspurity_createdatabase mspurity_createmsp mspurity_dimspredictpuritysingle mspurity_filterfragspectra mspurity_flagremove mspurity_frag4feature mspurity_puritya mspurity_purityx mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data			11640		bioconductor-mspurity		To update	UseGalaxy.cz10 UseGalaxy.eu10 UseGalaxy.fr11 UseGalaxy.no10
metfrag	2.4.5+galaxy3	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)			590		metfrag		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
metfrag-vis	2.4.5+galaxy0	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag			52		metfrag		To update	UseGalaxy.cz1 UseGalaxy.eu1
cfmid	33	cfmid	Competitive Fragmentation Modeling (CFM)			0		cfm		Up-to-date
xcms	4.4.0	abims_xcms_fillPeaks abims_xcms_group abims_xcms_refine abims_xcms_retcor abims_xcms_summary abims_xcms_xcmsSet msnbase_readmsdata xcms_export_samplemetadata xcms_merge xcms_plot_chromatogram xcms_plot_eic xcms_plot_raw		Biological imaging Data visualisation Metabolomics	Mass spectrum visualisation Label-free quantification Validation Chromatographic alignment Peak detection Chromatogram visualisation Data filtering	2728715	XCMS	bioconductor-xcms		Up-to-date	UseGalaxy.be6 UseGalaxy.cz10 UseGalaxy.eu12 UseGalaxy.fr12 UseGalaxy.no9 UseGalaxy.or11
w4mconcatenate	1.0.0+galaxy1	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables			4		r-base		To update	UseGalaxy.fr1
skyline2isocor	1.0.0	skyline2isocor	Converting skyline output to IsoCor input			115		skyline2isocor		Up-to-date	UseGalaxy.eu1 UseGalaxy.fr1
physiofit_manager	1.0.1	physiofit_data_manager	Handling of physiofit input files			9		physiofit_data_manager		Up-to-date	UseGalaxy.fr1
physiofit	3.4.0	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes			28		physiofit		Up-to-date	UseGalaxy.fr1
normalization	1.0.7+galaxy2	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data			3444		r-batch		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
nmr_preprocessing		NMR_Preprocessing NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction			2746		r-ggplot2		To update	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.no2 UseGalaxy.or2
2dnmrannotation	2.0.0+galaxy3	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra			57		r-batch		To update	UseGalaxy.fr1
nmr_annotation	3.0.0+galaxy1	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation			423		libgfortran		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
mzxmlshaper	1.0.0+galaxy1	mzxmlshaper	Convert mzML, mzXML or netCDF files to mzML or mzXML			502		r-base		To update	UseGalaxy.fr1
ms2snoop	2.2.1	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.			157		r-base		To update	UseGalaxy.fr1
mixmodel4repeated_measures	3.1.0+galaxy1	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model			305		r-lme4		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
kmd_hmdb_data_plot	1.0.0	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file			0		click		To update
isoplot	1.3.1	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments			137		jinja2		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1
ipo	1.10.0	ipo4retgroup ipo4xcmsSet	[W4M][LC-MS] IPO			0		bioconductor-ipo		To update
intensity_checks	2.0.1	intens_check	Statistical measures, number of missing values and mean fold change for metabolomics data.			7866		r-base		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
influx_si	7.0.1	influx_si	metabolic flux estimation based on [in]stationary labeling			18		influx_si		To update	UseGalaxy.fr1
influx_si_data_manager	1.0.2	influx_data_manager	Handling influx_si data inputs in Galaxy workflows			9		influx-si-data-manager		To update	UseGalaxy.fr1
genform		genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data			68		genform		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
gcms2isocor	0.2.1	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs			0				To update
correlation_analysis	1.0.1+galaxy2	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis			231		r-batch		To update	UseGalaxy.fr1
camera	1.48.0	abims_CAMERA_annotateDiffreport abims_CAMERA_combinexsAnnos CAMERA_findAdducts CAMERA_findIsotopes CAMERA_groupCorr CAMERA_groupFWHM				16515		r-snow		To update	UseGalaxy.be1 UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr6 UseGalaxy.no2 UseGalaxy.or2
wade	0.2.5+galaxy1	wade	identify regions of interest			0		wade		To update
tree_relabeler	1.1.0	tree_relabel	Relabels the tips of a newick formatted tree.			0		perl-bioperl		To update
stringmlst	1.1.0	stringmlst	Rapid and accurate identification of the sequence type (ST)			0		stringMLST		To update
staramr	0.11.0	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.	Microbiology Public health and epidemiology Infectious disease	Antimicrobial resistance prediction	51323	staramr	staramr		Up-to-date	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
srst2	0.3.7	srst2	Short Read Sequence Typing for Bacterial Pathogens			387		srst2		To update	UseGalaxy.cz1 UseGalaxy.eu1
spolpred	1.0.1	spolpred	A program for predicting the spoligotype from raw sequence reads			0		spolpred		To update
spatyper	0.3.3	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.			0		spatyper		Up-to-date
spades_fasta_header_fixer	1.1.2+galaxy1	spades_header_fixer	Fixes Spades Fasta ids			0		sed		To update
smalt	0.7.6	smalt	SMALT aligns DNA sequencing reads with a reference genome.			0		smalt		Up-to-date
sistr_cmd	1.1.3	sistr_cmd	SISTR in silico serotyping tool	Whole genome sequencing Immunoproteins and antigens Sequence assembly Zoology Public health and epidemiology	Genome assembly Visualisation Multilocus sequence typing	4863	SISTR	sistr_cmd		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
seqtk_nml	1.0.1	seqtk_nml_sample	Tool to downsample fastq reads			0		seqtk		To update
refseq_masher	0.1.2	refseq_masher_contains refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.			5661		refseq_masher		Up-to-date	UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
quasitools	0.7.0	aacoverage aavariants callcodonvar callntvar complexity_bam complexity_fasta consensus distance dnds drmutations hydra quality	A collection of tools for analysing Viral Quasispecies			14279		quasitools		Up-to-date	UseGalaxy.fr12 UseGalaxy.or12
pseudogenome	1.0.0	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.			0		perl-bioperl		To update
promer	1.2	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them			0		python		To update
pneumocat	1.2.1	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads			0		pneumocat		Up-to-date
plasmidspades	1.1	plasmidspades	Genome assembler for assemblying plasmid			0		spades		To update
suite_plasmid_profiler			Plasmid Profiler suite defining all dependencies for Plasmid Profiler			0				To update
plasmid_profiler	0.1.6	plasmid_profiler	Explores plasmid content in WGS data			0		r		To update
patrist	0.1.2	patrist	Extract Patristic Distance From a Tree			0		python		To update
pangolin	1.1.14	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages			19682		pangolin		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
mykrobe_parser	0.1.4.1	mykrobe_parseR	RScript to parse the results of mykrobe predictor.			0		r-base		To update
mrbayes	1.0.2	mrbayes	A program for the Bayesian estimation of phylogeny.			0		mrbayes		To update	UseGalaxy.be1 UseGalaxy.eu1
mob_suite	3.1.9	mob_recon mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies	Metagenomics Sequence assembly Genotype and phenotype Mobile genetic elements Genomics	Clustering Sequence analysis	193569	mob_suite	mob_suite		Up-to-date	UseGalaxy.cz2 UseGalaxy.eu2 UseGalaxy.fr2 UseGalaxy.or2
mauve_contig_mover	1.0.10	mauve_contig_mover	Order a draft genome relative to a related reference genome			0		mauve		To update
kat_sect	2.3	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.			0		kat		To update
kat_filter	2.3	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes			0		kat		To update
kaptive	0.3.0	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.			0		kaptive		To update
hivtrace	1.0.1	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.			0		hivtrace		To update
gnali	1.1.0	gnali	A tool to find nonessential, loss-of-function gene variants			0		gnali		Up-to-date
getmlst	0.1.4.1	getmlst	Download MLST datasets by species from pubmlst.org			0		srst2		To update
filter_spades_repeats	1.0.1	filter_spades_repeat	Remove short and repeat contigs/scaffolds			0		perl-bioperl		To update
feht	0.1.0	feht	Automatically identify makers predictive of groups.			0		feht		To update
fastqc_stats	1.2	FastQC_Summary	Summary multiple FastQC into a single tabular line report			0		perl-bioperl		To update
fasta_extract	1.1.0	fa-extract-sequence	extract single fasta from multiple fasta file			1837		perl-bioperl		To update
fasta2bed	1.0.0	fasta2bed	Convert multiple fasta file into tabular bed file format			0		perl-bioperl		To update
ectyper	2.0.0	ectyper	EC-Typer - in silico serotyping of Escherichia coli species	Whole genome sequencing Public health and epidemiology Sequence assembly Genotype and phenotype Workflows	Sequence assembly Read pre-processing Variant calling	16579	ectyper	ectyper		Up-to-date	UseGalaxy.cz1 UseGalaxy.eu1
csvtk	0.20.0	csvtk_awklike_filter csvtk_awklike_mutate csvtk_collapse csvtk_concat csvtk_convert csvtk_correlation csvtk_cut csvtk_filter csvtk_freq csvtk_gather csvtk_join csvtk_mutate csvtk_plot csvtk_replace csvtk_sample csvtk_separate csvtk_sort csvtk_split csvtk_summary csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files			124		csvtk		To update	UseGalaxy.fr1 UseGalaxy.or6
cryptogenotyper	1.0	CryptoGenotyper	CryptoGenotyper is a standalone tool to in-silico determine species and subtype based on SSU rRNA and gp60 markers.			11902		cryptogenotyper		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
concat_paired	0.2	concat_fastqs	Concatenate paired datasets			0				To update
combine_tabular_collection	0.1	combine	Combine Tabular Collection into a single file			0				To update
combine_assemblystats	1.0	combine_stats	Combine multiple Assemblystats datasets into a single tabular report			0		perl-getopt-long		To update
combine_json	0.1	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.			0				To update
collapse_collections	5.1.0	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection			99100		gawk		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1 UseGalaxy.or1
bundle_collections	1.3.0	bundle_collection	Tool to bundle up list collection into a single zip to be download			3600		perl-getopt-long		To update	UseGalaxy.fr1 UseGalaxy.or1
biohansel_bionumeric_converter	0.2.0	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form			0		pandas		To update
biohansel	2.4.0	biohansel	Heidelberg and Enteritidis SNP Elucidation			0		bio_hansel		To update
bamclipper	1.0.0	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.			0		bamclipper		Up-to-date
bam2mappingstats	1.1.0	bam2mappingstats	Generates mapping stats from a bam file.			0		perl		To update
assemblystats	1.1.0	assemblystats	Summarise an assembly (e.g. N50 metrics)			0		perl-bioperl		To update
abacas	1.1	abacas	Order and Orientate Contigs			0		mummer		To update	UseGalaxy.fr1
t_coffee	13.45.0.4846264	t_coffee	T-Coffee			9236		t-coffee		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
smina	1.0	smina	Scoring and Minimization with smina			549		smina		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
smart_domains	0.1.0	smart_domains	SMART domains			0		perl-bioperl		To update
replace_chromosome_names	0.1	replace_chromosome_names	Replace chromosome names			579		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
rdock	1.0	rdock	Docking ligands to proteins and nucleic acids			0		rDock		To update
plotheatmap	1.0	plotheatmap	Plot heatmap of gene expression data			0		bioconductor-preprocesscore		To update
miranda	3.3a+galaxy1	miranda	Finds potential target sites for miRNAs in genomic sequences			7099		miranda		To update	UseGalaxy.eu1 UseGalaxy.fr1
lotus2	2.32	lotus2	LotuS2 OTU processing pipeline	Metagenomics Taxonomy Microbial ecology	Sequence feature detection DNA barcoding	1747	lotus2	lotus2		To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
hcluster_sg_parser	0.3.0	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids			297		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
hcluster_sg	0.5.1.1	hcluster_sg	Hierarchically clustering on a sparse graph			287		hcluster_sg		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
gstf_preparation	0.4.3	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow			401		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
gblocks	0.91b	gblocks	Gblocks			580		gblocks		Up-to-date	UseGalaxy.be1 UseGalaxy.fr1 UseGalaxy.or1
export_to_cluster	0.1.0	export_to_cluster	Export datasets to cluster			0		python		To update
ete	3.1.3	ete_gene_csv_finder ete_genetree_splitter ete_homology_classifier ete_init_taxdb ete_lineage_generator ete3_mod ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	Phylogenetics	Phylogenetic analysis Phylogenetic tree editing	985	ete	ete3		To update	UseGalaxy.cz7 UseGalaxy.eu7 UseGalaxy.fr7 UseGalaxy.no7
blast_parser	0.2.0	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input			563		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
apoc	1.0+galaxy1	apoc	Large-scale structural comparison of protein pockets			9		apoc		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1 UseGalaxy.or1
treebest_best	1.9.2.post0	treebest_best	TreeBeST best	Phylogenetics	Phylogenetic tree visualisation Phylogenetic analysis Phylogenetic inference (from molecular sequences)	1025	treebest	treebest		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.no1
gafa	0.4.1	gafa	Gene Align and Family Aggregator			47		python		To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.no1
Ensembl-REST	1.0.0	get_feature_info get_genetree get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.			2927		python		To update	UseGalaxy.cz3 UseGalaxy.eu3 UseGalaxy.no3
peptimapper	2.1	peptimapper_clustqualify peptimapper_clust_to_gff peptimapper_pep_match peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes			6				To update	UseGalaxy.fr4
openlabcds2csv	0.1.0	openlabcds2csv	Creates a summary of several "Internal Standard Report" OpenLabCDS results.			0		openjdk		To update
miranda2asko	0.2	miranda2asko	Converts miRanda output into AskOmics format			0		perl		To update
meneco	1.5.2	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network			0		meneco		Up-to-date
logol	1.7.8	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence			0		logol		Up-to-date
helixer	0.3.3	helixer	Gene calling with Deep Neural Networks	Sequence analysis Gene transcripts	Gene prediction Genome annotation	1013	helixer			To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
get_pairs	0.3	get_pairs	Separate paired and unpaired reads from two fastq files			0		python		To update
gcms2isocor	0.1.0	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor			0		openjdk		To update
feelnc2asko	0.1	feelnc2asko	Convert FeelNC GTF to GFF3			0		perl-bioperl		To update
braker3	3.0.8	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	RNA-Seq Genomics Structure prediction Sequence analysis	Genome annotation Gene prediction	3928	braker3			To update	UseGalaxy.cz1 UseGalaxy.eu1 UseGalaxy.fr1 UseGalaxy.or1
braker	2.1.6	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .			217				To update	UseGalaxy.be1 UseGalaxy.cz1 UseGalaxy.eu1
baric_archive	1.1.0	baric_archive_rennes baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.			16				To update	UseGalaxy.fr2
askor_de	0.2	askor_de	AskoR links EdgeR and AskOmics			3		bioconductor-limma		To update