Galaxy US Tools

Download and Extract Reads in BAM Download and Extract Reads in FASTQ Download run data EBI SRA EBI Search EGA Download Client Faster Download and Extract Reads in FASTQ IEDB NCBI Accession Download NCBI Datasets Gene NCBI Datasets Genomes Protein Database Downloader UCSC Main UniProt Unipept Upload File fastq-dl pysradb search

Export datasets

Apply rules Build list Collapse Collection Column join Convert sample sheet Duplicate file to collection Extract dataset Extract element identifiers Filter collection Filter empty datasets Filter failed datasets Filter null elements Flat Cross Product Flatten collection Harmonize two collections Keep success Merge collections Nest collection Nested Cross Product Relabel identifiers Sample sheet to tabular Sort collection Split Paired and Unpaired Split file Tag elements Unzip collection Zip collections

Calculate numeric parameter value Compose text parameter value Map parameter value Parse parameter value Pick parameter value

Add column Add column Add input name as column Add line to file Advanced Cut Change Case Column Regex Find And Replace Column arrange Compute Concatenate datasets Concatenate multiple datasets Concatenate multiple datasets Concatenate multiple datasets or collections Condense Convert Create single interval Create text file Cut Filter Tabular Join Line/Word/Character count Merge Columns Multi-Join Number lines Paste Query Tabular Rebase GFF3 features Regex Find And Replace Remove beginning Remove columns Replace Replace Text Replace Text Replace column SQLite to tabular Search in textfiles Secure Hash / Message Digest Select first Select first Select last Select last Select random lines Sort Sort Column Order Sort a row Split by group Table Compute Text reformatting Text transformation Trim Unfold UniProt Unique Unique Unique lines annotateMyIDs cast diff jq melt tac

Bigwig outliers to bed features Extract features Filter Filter GFF data by attribute Filter GFF data by feature count Filter GTF data by attribute values_list Select Sub-sample sequences files

Compare two Datasets Group Join two Datasets Subtract Whole Dataset

Datamash Reverse Transpose

Barcode Splitter Clip Collapse Combine FASTA and QUAL Compute sequence length Concatenate Cutadapt FASTA Merge Files and Filter Unique Sequences FASTA Width FASTA-to-Tabular FASTQ Groomer FASTQ Masker FASTQ Quality Trimmer FASTQ Trimmer FASTQ de-interlacer FASTQ interlacer FASTQ joiner FASTQ splitter FLASH Fasta Statistics Fasta regular expression finder Filter FASTA Filter FASTQ Filter by quality Filter sequences by ID Filter sequences by length Gene length and GC content Manipulate FASTQ Nucleotide subsequence search Pear Quality format converter RNA/DNA Remove sequencing artifacts Rename sequences Reverse-Complement Select high quality segments SeqKit grep SeqKit translate Seqkit Split2 Sickle Split Fasta Tabular-to-FASTA Trim Galore! Trim sequences UMI-tools count UMI-tools deduplicate UMI-tools extract UMI-tools group UMI-tools whitelist faSplit fastp fastq-join filtlong

Compute quality statistics Draw nucleotides distribution chart Draw quality score boxplot FASTQ Summary Statistics FASTQ info FASTQE Falco FastQC MultiQC PRINSEQ Trimmomatic

BAM-to-SAM BamUtil clipOverlap Convert SAM Filter BAM Filter SAM Filter SAM or BAM, output SAM or BAM Filter mapped reads Filter pileup Generate pileup Operate on and transform BAM Pileup-to-Interval QualiMap BamQC QualiMap Multi-Sample BamQC RmDup SAM-to-BAM Sambamba flagstat Sambamba markdup Sambamba merge Sambamba sort Samtools ampliconclip Samtools bedcov Samtools calmd Samtools collate Samtools coverage Samtools depth Samtools fastx Samtools fixmate Samtools flagstat Samtools idxstats Samtools markdup Samtools merge Samtools mpileup Samtools phase Samtools reheader Samtools sort Samtools split Samtools stats Samtools view Slice Split Split Split BAM by read tag value Split BAM by reads mapping status Split BAM by reference Split BAM into paired- and single-end mosdepth revertR2orientationInBam

bedops sort-bed bedtools AnnotateBed bedtools BAM to BED bedtools BED to BAM bedtools BED to IGV bedtools BED12 to BED6 bedtools BEDPE to BAM bedtools ClosestBed bedtools ClusterBed bedtools ComplementBed bedtools Compute both the depth and breadth of coverage bedtools Convert from BAM to FastQ bedtools ExpandBed bedtools FisherBed bedtools FlankBed bedtools Genome Coverage bedtools GroupByBed bedtools Intersect intervals bedtools JaccardBed bedtools LinksBed bedtools MakeWindowsBed bedtools MapBed bedtools MaskFastaBed bedtools Merge BedGraph files bedtools MergeBED bedtools MultiCovBed bedtools Multiple Intersect bedtools NucBed bedtools OverlapBed bedtools RandomBed bedtools ReldistBed bedtools ShuffleBed bedtools SlopBed bedtools SortBED bedtools SpacingBed bedtools SubtractBed bedtools TagBed bedtools WindowBed bedtools getfasta

Annotate Slice VCF VCF-BEDintersect: VCF-VCFintersect: VCFaddinfo: VCFannotate: VCFannotateGenotypes: VCFbreakCreateMulti: VCFcheck: VCFcombine: VCFcommonSamples: VCFdistance: VCFdistance: VCFfilter: VCFfixup: VCFflatten: VCFgenotype-to-haplotype: VCFgenotypes: VCFhetHomAlleles: VCFleftAlign: VCFprimers: VCFrandomSample: VCFselectsamples: VCFsort: VCFtoTab-delimited: VcfAllelicPrimitives: bcftools List Samples bcftools annotate bcftools call bcftools cnv bcftools concat bcftools consensus bcftools convert from vcf bcftools convert to vcf bcftools counts bcftools csq bcftools dosage bcftools fill-AN-AC bcftools fill-tags bcftools filter bcftools fixploidy bcftools gtcheck bcftools impute-info bcftools isec bcftools mendelian2 bcftools merge bcftools missing2ref bcftools mpileup bcftools norm bcftools query bcftools reheader bcftools roh bcftools setGT bcftools stats bcftools tag2tag bcftools view

Clair3 Collector’s curve Extract FASTQ Extract nanopore events Extract reads Extract time Flye Generate box-whisker Generate histogram Get longest read NanoPlot Plot performance Plot signals Porechop Pycoqc Read length statistics Show nucleotide Show quality medaka consensus pipeline medaka inference tool medaka variant pipeline medaka vcf tool

BAM BED GFF coverage bigWigs BED-to-GFF BED-to-bigBed Compress file(s) Convert BAM Convert BAM to ScIdx Convert GTF to BED12 Convert gffCompare annotated GTF to BED Create InterMine Interchange CrossMap BAM CrossMap BED CrossMap GFF CrossMap VCF CrossMap Wig Excel to Tabular FASTA-to-Tabular FASTQ to FASTA FASTQ to FASTA FASTQ to Tabular GFA to FASTA GFF-to-BED Image Montage MAF to BED MAF to FASTA MAF to Interval PacBio bam2fastx RDS to tabular SFF converter Tabular to FASTQ Tabular-to-FASTA ToolDistillator ToolDistillator Summarize Unzip axtToMaf bax2bam bed to protein map faToVcf gffread mafToAxt msconvert mz to sqlite netToAxt twoBitToFa wigtobigwig

Convert genome coordinates

Aggregate datapoints Base Coverage Cluster Complement Concatenate Coverage Fetch closest non-overlapping feature Gene BED To Exon/Intron/Codon BED Get flanks Intersect Join Merge Subtract Translate BED transcripts Wiggle-to-Interval

Extract Genomic DNA Extract MAF by block number Extract Pairwise MAF blocks Filter MAF Filter MAF blocks Filter MAF blocks Join MAF blocks MAF Coverage Stats Reverse Complement Stitch Gene blocks Stitch MAF blocks

AEGeAn ParsEval ALNchain Bandage Image Bandage Info Bionano Hybrid Scaffold BlobToolKit Create assemblies with Unicycler DISCO FastGA FastK FastK Histex FastK Logex Filter and merge GenomeScope HalfDeep Hifiasm IDBA-HYBRID IDBA-TRAN IDBA-UD LexicMap Index LexicMap Search MEGAHIT Merqury Merqury histogram plot Meryl Meryl Meryl Meryl Meryl Meryl Meryl Meryl MitoHiFi NextDenovo Pairtools Stats Pairtools dedup Pairtools parse Pairtools sort Pairtools split Pretext Snapshot PretextMap Pretextgraph Purge overlaps Quast Racon RagTag RefSeq Masher Contains RefSeq Masher Matches SALSA SPAdes Shovill Smudgeplot Teloscope VGP Chromosome Assignment VGP SAK Generation VGP Split AGP VelvetOptimiser YAHS biosyntheticSPAdes coronaSPAdes gfastats kmindex build kmindex query metaSPAdes metaplasmidSPAdes metaviralSPAdes miniasm pilon plasmidSPAdes rnaQUAST rnaSPAdes rnaviralSPAdes velvetg velveth

ABRicate ABRicate List ABRicate Summary AGAT AMRFinderPlus Antismash Augustus BRAKER3 Bakta BlastXML to gapped GFF3 Busco CPAT Cojac: mutbamscan Cojac: tabmut Convert XMFA to gapped GFF3 CoreProfiler allele_calling DeepARG short reads Exonerate Filter with SortMeRNA Find Nested Alternate ORFs (nAlt-ORFs) Freyja: Aggregate and visualize Freyja: Demix Funannotate compare Funannotate functional Funannotate predict annotation GOEnrichment GOSlimmer GSEApy Enrichr Genbank to GFF3 Genome annotation statistics Get Codon and Bicodon frequency Get Codon frequency Groot Gubbins Helixer ICEscreen ISEScan Integron Finder InterProScan KEGG ORA KOBAS Annotate KOBAS Identify Liftoff List spaln parameter tables MITOS2 MLST MLST List MMseqs2 taxonomy Maker Map annotation ids Miniprot align Miniprot index NCBI EGAPx NCBI EGAPx execute NCBI EGAPx prepare input Nucleolar localization sequence Detector (NoD) OMArk ORFipy OptiType OrthoFinder PfamScan PlasmidFinder Prodigal Gene Predictor Prokka Psauron Read It and Keep Red RepeatMasker RepeatModeler Roary STR to bed Spaln: align cDNA or Protein to genome TAPScan Classify TB Variant Filter TB Variant Report TB-Profiler Profile TETyper Table to GFF3 Train Augustus Train SNAP TransTermHP WindowMasker mkcounts WindowMasker ustat alimask argNorm compleasm fargene fgsea gProfiler Convert gProfiler GOSt gProfiler Orth gProfiler Random gProfiler SNPense hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmscan hmmsearch jackhmmer nhmmer nhmmscan phmmer progressiveMauve seq2HLA socru staramr tRNA and tmRNA

Align sequences BBTools: BBMap BWA-MEM2 BWA-MEM2 indexer Batched LASTZ Bowtie2 KegAlign LASTZ LASTZ_D Map with BWA Map with BWA-MEM Map with minimap2 MethylDackel Parse blast XML output RNA STARSolo STAR-Fusion SegAlign Winnowmap axtChain bwameth chainAntiRepeat chainNet chainPreNet chainSort chainSwap metilene netChainSubset netFilter netSyntenic

Add LoFreq alignment quality scores Arriba Arriba Draw Fusions Arriba Get Filters BamLeftAlign Call variants DeepVariant ExomeDepth FASTA from allele counts Finds SNP sites FreeBayes GATK4 Mutect2 Insert indel qualities JasmineSV Lofreq filter MAF boxplot Mutate Codons Naive Variant Caller (NVC) Phylorelatives Realign reads SNP distance matrix SnpEff build: SnpEff chromosome-info: SnpEff databases: SnpEff download: SnpEff eff: SnpSift Annotate SnpSift CaseControl SnpSift Extract Fields SnpSift Filter SnpSift GeneSets SnpSift Intervals SnpSift Variant Type SnpSift dbNSFP SnpSift rmInfo SnpSift vcfCheck Strelka Germline Strelka Somatic VarScan VarScan copynumber VarScan mpileup VarScan somatic Variant Annotator Variant Frequency Plot basil bcftools color-chrs bcftools frameshifts faToVcf ococo sniffles snippy snippy-clean_full_aln snippy-core

BAM filter CWPair2 ChIPseeker DiffBind Fasta nucleotide color plot GeneTrack Genrich MACS2 bdgbroadcall MACS2 bdgcmp MACS2 bdgdiff MACS2 bdgpeakcall MACS2 callpeak MACS2 filterdup MACS2 predictd MACS2 randsample MACS2 refinepeak MultiGPS Paired-end histogram RepMatch Resize coordinate window SEACR SICER Tag pileup frequency

Align reads and estimate abundance Alleyoop Annotate DESeq2/DEXSeq output tables BREW3R.r BlockClust Build expression matrix CEMiTool Calculate a Heinz score ChiRA collapse ChiRA extract ChiRA map ChiRA merge ChiRA qauntify Compute contig Ex90N50 statistic and Ex90 transcript count Cross-contamination Barcode Filter DESeq2 DEXSeq DEXSeq-Count Diamond Diamond makedb Diamond view Differential expression analysis EGSEA FEELnc Filter Combined Transcripts Filter low expression transcripts Fit a BUM model Generate SuperTranscripts Generate gene to transcript map Get RT Stop Counts GffCompare HISAT2 IDR Identify optimal scoring subnetwork IsoformSwitchAnalyzeR Iterative Mapping Kallisto pseudo Kallisto quant MiRDeep2 MiRDeep2 Mapper MiRDeep2 Quantifier QualiMap Counts QC QualiMap RNA-Seq QC RNA STAR RNA Structure Prediction RNASeq samples quality check Reactivity Calculation Remove Unwanted Variation Sailfish Salmon quant Seurat Slamdunk StringTie StringTie merge TargetFinder TransDecoder Trinity Trinotate Visualize blockbuster cummeRbund edgeR featureCounts goseq htseq-count limma maSigPro ngsderive strandedness pizzly plotDEXSeq scPipe tximport

Automated multiple sequence ClustalW DNAdiff Delta-Filter Extract MAF blocks Kc-Align MAF Coverage Stats MAFFT MAFFT add MMseqs2 easy-linclust MSABOOT Mummer Mummerplot Nucmer SINA Show-Coords Stitch Gene blocks cawlign mafAddIRows mafCoverage mafFetch mafFilter mafFrags mashmap

BEAM DAVID FunDO GPASS HVIS LD LPS MasterVar to pgSnp PASS Separate pgSnp alleles VCF to pgSnp g:Profiler plink snpFreq

Analysis of artifacts with Tasmanian FASTTREE IQ-TREE Join neighbors Merge matching reads PhyKIT metrics PhyKit - Alignment- and tree-based functions PhyKit - Alignment-based functions PhyKit - Tree-based functions TN93 TN93 Cluster TN93 Filter

Assign weighted-average Estimate Indel Rates Estimate microsatellite mutability Extract Orthologous Microsatellites Feature coverage Fetch Indels Fetch Indels Fetch substitutions Fit HMM Heatmap Karyotype Plotting tool Make windows Mask CpG/non-CpG sites

hifive

Bio-TraDis Essentiality Predictions Bio-TraDis counts to gene insertion data Bio-TraDis reads to counts Convert GFF3 TRANSIT Gumbel TRANSIT HMM TRANSIT Resampling TRANSIT Tn5Gaps

DBKit Create DBKit Create DBKit Extract DBKit Extract DBKit Merge DBKit Merge HHsearch SPRING Cross SPRING MCC SPRING Map SPRING Min-Z SPRING Model SPRING Model-All

MAGeCK count MAGeCK mle MAGeCKs test

Ocean biodiversity indicators

NCBI FCS Adaptor NCBI FCS GX

RAxML

Anova Biosigner Calculate sequence complexity Compute RCVE Compute partial R square Count Count GFF Features Draw ROC plot Feature-wise Correlation Tests Generate A Matrix GraphEmbed Heatmap Kernel Canonical Correlation Analysis Kernel Principal Component Analysis MINE Multivariate Nonparametric rank tests Perform Best-subsets Regression Perform LDA Perform Linear Regression Perform affine image registration (landmark-based) Principal Component Analysis RGCCA Rolling window Sequence composition Sparse Matrix Functions Summary Statistics T Test for Two Samples Transformation Univariate Wavelet variance rdeval rdeval report

Build Deep learning Batch Training Models Calculate metrics Calculate metrics Create a deep learning model architecture Create a model to recommend tools Create deep learning model Deep learning training and evaluation Discriminant Analysis Ensemble methods Estimator attributes Evaluate a Fitted Model Evaluate pairwise distances Feature Selection Fit a Pipeline, Ensemble Flexynesis Flexynesis Inference Flexynesis cBioPortal import Flexynesis plot Flexynesis utils Generalized linear models Generate Generic Learner Config Creator Generic Learner Evaluate Generic Learner Experiment Generic Learner Hyperopt Generic Learner Predict Generic Learner Render Config Generic Learner Train Generic Learner Visualize Hyperparameter Search Image Learner LightGBM Model Prediction Model Validation Multimodal Learner Nearest Neighbors Classification Numeric Clustering Pipeline Builder Preprocess Principal component analysis PyCaret Predictor/Evaluator Sparse Matrix Functions Split Dataset Stacking Ensembles Support vector machines (SVMs) Tabular Learner To categorical Train, Test and Evaluation chopin2

BAM Coverage Plotter Build custom track Circos Circos Builder Circos: Alignments to links Circos: Bundle Links Circos: Interval to Circos Text Labels Circos: Interval to Tiles Circos: Link Density Track Circos: Resample 1/2D data Circos: Stack bigWigs as Histogram Circos: Table viewer Circos: bigWig to Scatter Export to GraPhlAn GC Skew GMAJ Generation, personalization and annotation of tree GraPhlAn Heatmap w ggplot Histogram Histogram with ggplot2 JBrowse JBrowse - Data Directory to Standalone JBrowse2 Krona pie chart MUMmer dotplot Machine Learning Visualization Extension Newick Display PCA plot w ggplot2 Pairwise intersection Parallel Coordinates Plot Pathview Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Plotting tool Scatterplot Scatterplot with ggplot2 UpSet diagram VCF to MAF Custom Track Venn Diagram Violin plot w ggplot2 Visualize with Krona Volcano Plot autogenjb2 heatmap2 hicPlotTADs pyGenomeTracks rtsne

Data Analysis Agent Interactive BlobToolKit Interactive JupyterLab Notebook Panoply Pavian Phinch Visualisation Phyloseq PhysiCell Studio Qiskit Jupyter notebook QuPath RStudio

Check STR motif compatibility between reference and read STRs Combine mapped faux paired-end reads Combine read profile probabilities Convert informative read depth to sequencing depth Correct genotype for STR errors Evaluate the probability of the allele combination to generate read profile Fetch bases flanking Generate all possible combination of STR length profile Read name modifier STR detection Select uninterrupted STRs

Align.check Align.seqs Amova Anosim Bin.seqs Biom.info Chimera.bellerophon Chimera.ccode Chimera.check Chimera.perseus Chimera.pintail Chimera.slayer Chimera.uchime Chimera.vsearch Chop.seqs Classify.otu Classify.rf Classify.seqs Classify.tree Clearcut Cluster Cluster.classic Cluster.fragments Cluster.split Collect.shared Collect.single Consensus.seqs Cooccurrence Corr.axes Count.groups Count.seqs Create.database Degap.seqs Deunique.seqs Deunique.tree Dist.seqs Dist.shared Fastq.info Filter.seqs Filter.shared Get.communitytype Get.coremicrobiome Get.dists Get.group Get.groups Get.label Get.lineage Get.mimarkspackage Get.otulabels Get.otulist Get.oturep Get.otus Get.rabund Get.relabund Get.sabund Get.seqs Get.sharedseqs Hcluster Heatmap.bin Heatmap.sim Homova Indicator Lefse Libshuff List.otulabels List.seqs Make Design Make.biom Make.contigs Make.fastq Make.group Make.lefse Make.lookup Make.shared Make.sra Mantel Merge.count Merge.files Merge.groups Merge.sfffiles Merge.taxsummary Metastats Mimarks.attributes Nmds Normalize.shared Otu.association Otu.hierarchy Pairwise.seqs Parse.list Parsimony Pca Pcoa Pcr.seqs Phylo.diversity Phylotype Pre.cluster Primer.design Rarefaction.shared Rarefaction.single Remove.dists Remove.groups Remove.lineage Remove.otulabels Remove.otus Remove.rare Remove.seqs Rename.seqs Reverse.seqs Screen.seqs Sens.spec Seq.error Sffinfo Shhh.flows Shhh.seqs Sort.seqs Split.abund Split.groups Sub.sample Summary.qual Summary.seqs Summary.shared Summary.single Summary.tax Taxonomy-to-Krona Tree.shared Trim.flows Trim.seqs Unique.seqs Venn unifrac.unweighted unifrac.weighted

qiime2 alignment mafft qiime2 alignment mafft-add qiime2 alignment mask qiime2 composition add-pseudocount qiime2 composition ancom qiime2 composition ancombc qiime2 composition tabulate qiime2 cutadapt demux-paired qiime2 cutadapt demux-single qiime2 cutadapt trim-paired qiime2 cutadapt trim-single qiime2 dada2 denoise-ccs qiime2 dada2 denoise-paired qiime2 dada2 denoise-pyro qiime2 dada2 denoise-single qiime2 deblur denoise-16S qiime2 deblur denoise-other qiime2 deblur visualize-stats qiime2 demux emp-paired qiime2 demux emp-single qiime2 demux filter-samples qiime2 demux subsample-paired qiime2 demux subsample-single qiime2 demux summarize 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-distance-matrix qiime2 diversity mantel qiime2 diversity pcoa qiime2 diversity pcoa-biplot qiime2 diversity procrustes-analysis qiime2 diversity tsne qiime2 diversity umap 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 qiime2 emperor biplot qiime2 emperor plot qiime2 emperor procrustes-plot 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 vsearch-global 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 presence-absence qiime2 feature-table rarefy qiime2 feature-table relative-frequency qiime2 feature-table rename-ids qiime2 feature-table subsample qiime2 feature-table summarize qiime2 feature-table tabulate-seqs qiime2 feature-table transpose qiime2 fragment-insertion classify-otus-experimental qiime2 fragment-insertion filter-features qiime2 fragment-insertion sepp qiime2 gneiss assign-ids qiime2 gneiss correlation-clustering qiime2 gneiss dendrogram-heatmap qiime2 gneiss gradient-clustering qiime2 gneiss ilr-hierarchical qiime2 gneiss ilr-phylogenetic qiime2 gneiss ilr-phylogenetic-differential qiime2 gneiss ilr-phylogenetic-ordination 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 qiime2 metadata distance-matrix qiime2 metadata shuffle-groups qiime2 metadata tabulate 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 qiime2 quality-control bowtie2-build 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 qiime2 quality-filter q-score 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 qiime2 taxa barplot qiime2 taxa collapse qiime2 taxa filter-seqs qiime2 taxa filter-table qiime2 tools export qiime2 tools import qiime2 tools import-fastq 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

AddCommentsToBam AddOrReplaceReadGroups BedToIntervalList CleanSam Collect Alignment Summary Metrics CollectBaseDistributionByCycle CollectGcBiasMetrics CollectHsMetrics CollectInsertSizeMetrics CollectRnaSeqMetrics CollectWgsMetrics Downsample SAM/BAM EstimateLibraryComplexity FastqToSam FilterSamReads FixMateInformation MarkDuplicates MarkDuplicatesWithMateCigar MeanQualityByCycle MergeBamAlignment MergeSamFiles NormalizeFasta Picard Collect Sequencing Artifact Metrics QualityScoreDistribution ReorderSam ReplaceSamHeader RevertOriginalBaseQualitiesAndAddMateCigar RevertSam SamToFastq SortSam ValidateSamFile

bamCompare bamCoverage bamPEFragmentSize bigwigAverage bigwigCompare computeGCBias computeMatrix correctGCBias multiBamSummary multiBigwigSummary plotCorrelation plotCoverage plotEnrichment plotFingerprint plotHeatmap plotPCA plotProfile

antigenic backtranseq banana biosed btwisted cai cai custom chaos charge checktrans chips cirdna codcmp coderet compseq cpgplot cpgreport cusp cutseq dan degapseq descseq diffseq digest dotmatcher dotpath dottup dreg einverted epestfind equicktandem est2genome etandem extractfeat extractseq freak fuzznuc fuzzpro fuzztran garnier geecee getorf helixturnhelix hmoment iep infoseq isochore lindna marscan maskfeat maskseq matcher megamerger merger msbar needle newcpgreport newcpgseek newseq noreturn notseq nthseq octanol oddcomp palindrome pasteseq patmatdb pepcoil pepinfo pepnet pepstats pepwheel pepwindow pepwindowall plotcon plotorf polydot preg prettyplot prettyseq primersearch revseq seqmatchall seqret showfeat shuffleseq sigcleave sirna sixpack skipseq splitter supermatcher syco tcode textsearch tmap tranalign transeq trimest trimseq twofeat union vectorstrip water wobble wordcount wordmatch

BLAST XML to tabular NCBI BLAST+ blastdbcmd entry(s) NCBI BLAST+ blastn NCBI BLAST+ blastp NCBI BLAST+ blastx NCBI BLAST+ convert2blastmask NCBI BLAST+ database info NCBI BLAST+ dustmasker NCBI BLAST+ makeblastdb NCBI BLAST+ makeprofiledb NCBI BLAST+ rpsblast NCBI BLAST+ rpstblastn NCBI BLAST+ segmasker NCBI BLAST+ tblastn NCBI BLAST+ tblastx NCBI get species taxids

Annotate DRHIP HyPhy-BGM HyPhy-BUSTED HyPhy-CFEL HyPhy-CLN HyPhy-Conv HyPhy-FADE HyPhy-FEL HyPhy-FUBAR HyPhy-GARD HyPhy-MEME HyPhy-PRIME HyPhy-RELAX HyPhy-SLAC HyPhy-SM2019 HyPhy-Summary HyPhy-aBSREL Remove terminal stop codons Replace ambiguous codons sarscov2formatter sarscov2summary

BAM to Wiggle BAM/SAM Mapping Stats Clipping Profile Deletion Profile FPKM Count Gene Body Coverage (BAM) Gene Body Coverage (Bigwig) Hexamer frequency Infer Experiment Inner Distance Insertion Profile Junction Annotation Junction Saturation Mismatch Profile RNA fragment size RPKM Saturation Read Distribution Read Duplication Read GC Read NVC Read Quality Transcript Integrity Number

MiModD Convert MiModD Coverage Statistics MiModD Deletion Calling (for PE data) MiModD Extract Variant Sites MiModD File Information MiModD NacreousMap MiModD Read Alignment MiModD Rebase Sites MiModD Reheader MiModD Report Variants MiModD Run Annotation MiModD Sort MiModD VCF Filter MiModD Variant Calling

Plot Scanpy BBKNN Scanpy ComBat Scanpy MNN Scanpy Plot Scrublet Scanpy Scrublet Seurat UMAP

chicAggregateStatistic chicDifferentialTest chicExportData chicPlotViewpoint chicQualityControl chicSignificantInteractions chicViewpoint chicViewpointBackgroundModel hicAdjustMatrix hicAggregateContacts hicAverageRegions hicBuildMatrix hicCompareMatrices hicCompartmentalization hicConvertFormat hicCorrectMatrix hicCorrelate hicDetectLoops hicDifferentialTAD hicFindRestSite hicFindTADs hicHyperoptDetectLoops hicInfo hicInterIntraTAD hicMergeDomains hicMergeLoops hicMergeMatrixBins hicNormalize hicPCA hicPlotAverageRegions hicPlotDistVsCounts hicPlotMatrix hicPlotSVL hicPlotViewpoint hicQuickQC hicSumMatrices hicTADClassifier hicTrainTADClassifier hicTransform hicValidateLocations scHicAdjustMatrix scHicCluster scHicClusterCompartments scHicClusterMinHash scHicClusterSVL scHicConsensusMatrices scHicCorrectMatrices scHicCreateBulkMatrix scHicDemultiplex scHicInfo scHicMergeMatrixBins scHicMergeToSCool scHicNormalize scHicPlotClusterProfiles scHicPlotConsensusMatrices scHicQualityControl

Call specific mutations in reads: DCS mutations to SSCS stats: DCS mutations to tags/reads: Du Novo: Align families Du Novo: Check input Du Novo: Correct barcodes Du Novo: Make consensus reads Du Novo: Make families FSD Before/After: FSD regions: FSD: Sequence Content Trimmer TD:

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

Monocle3 create Monocle3 diffExp Monocle3 learnGraph Monocle3 orderCells Monocle3 partition Monocle3 plotCells Monocle3 preprocess Monocle3 reduceDim Monocle3 top markers

GEMINI actionable_mutations GEMINI amend GEMINI annotate GEMINI burden GEMINI database info GEMINI de_novo GEMINI inheritance pattern GEMINI interactions GEMINI load GEMINI lof_sieve GEMINI query GEMINI set_somatic GEMINI stats

BBTools: BBMap BBTools: BBMerge BBTools: BBNorm BBTools: BBduk BBTools: Tadpole BBTools: call variants

IWTomics Load IWTomics Plot with Threshold IWTomics Test

MiGMAP pRESTO AlignSets pRESTO AssemblePairs pRESTO BuildConsensus pRESTO CollapseSeq pRESTO FilterSeq pRESTO MaskPrimers pRESTO PairSeq pRESTO ParseHeaders pRESTO ParseLog pRESTO Partition pRESTOr AbSeq3 Report

AssemblyPostProcessor GeneFamilyAligner GeneFamilyClassifier GeneFamilyIntegrator GeneFamilyPhylogenyBuilder KaKsAnalysis KsDistribution

FIMO MEME MEME psp-gen MEME-ChIP Sequence Logo longdust

Run SCCAF SCCAF Assesment SCCAF Assesment Merger SCCAF mulitple regress out

Seurat CreateSeuratObject Seurat Export2CellBrowser Seurat FilterCells Seurat FindClusters Seurat FindMarkers Seurat FindNeighbours Seurat FindVariableGenes Seurat NormaliseData Seurat Plot dimension reduction Seurat Read10x Seurat RunPCA Seurat RunTSNE Seurat ScaleData

Nextclade Pangolin SnpEff eff: VIBRANT ivar consensus ivar filtervariants ivar getmasked ivar removereads ivar trim ivar variants snipit

Add metadata Beta Diversity Binette Biobox add taxid Bracken CAMI AMBER CAMI AMBER add length column CAMI AMBER convert to biobox CAT add_names CAT bins CAT contigs CAT prepare CAT summarise COMEBin CONCOCT CONCOCT: Cut up contigs CONCOCT: Extract a fasta file CONCOCT: Generate the input coverage table CONCOCT: Merge cut clusters Calculate KEGG Pathways completeness Calculate contig depths 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 CheckV end to end Combine MetaPhlAn and HUMAnN outputs Combine MetaPhlAn2 and HUMAnN2 outputs Convert Convert Kraken Converts genome bins in fasta format CoverM contig CoverM genome Create phyloseq object Create phyloseq object DAS Tool DefenseFinder Diamond Diamond makedb Diamond view GTDB-Tk Classify genomes HUMAnN KneadData Kraken Kraken taxonomic report Kraken-biom Kraken-filter Kraken-mpa-report Kraken-report Kraken-translate Kraken2 Krakentools: Calculates alpha diversity Krakentools: Combine multiple Kraken reports Krakentools: Convert kraken report file Krakentools: Convert kraken report file Krakentools: Extract Kraken Reads By ID Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) Krona pie chart MAPseq Map SNV MaxBin2 Merge Merging paired-end Illumina reads (SeqPrep, modified for use with MGnify piplines) MetaBAT2 MetaPhlAn NCBI-GTDB map Name2taxid Nonpareil PHI toolkit report Phyloseq: plot alpha diverstiy measure Phyloseq: plot ordination PlasFlow RGI bwt RGI main Recentrifuge Regroup Rename features Renormalize Resistance Gene Identifier (RGI) Salmonella Subtyping SameStr Compare SameStr Convert SameStr Extract SameStr Filter SameStr Merge SameStr Stats SameStr Summarize SemiBin Split a HUMAnN table Unpack pathway abundances VALET VAPOR VSearch alignment VSearch chimera detection VSearch clustering VSearch dereplication VSearch masking VSearch search VSearch shuffling VSearch sorting Vegan Diversity Vegan Fisher Alpha Vegan Rarefaction ampvis2 load cd-hit-dup checkm2 dRep compare dRep dereplicate dada2: assignTaxonomy and addSpecies dada2: dada dada2: filterAndTrim dada2: learnErrors dada2: makeSequenceTable dada2: mergePairs dada2: plotComplexity dada2: plotQualityProfile dada2: removeBimeraDenovo dada2: sequence counts geNomad iPHoP predict index kMetaShot khmer: Abundance Distribution khmer: Abundance Distribution (all-in-one) khmer: Count Median khmer: Extract partitions khmer: Filter reads khmer: Filter reads khmer: Normalize By Median khmer: Sequence partition all-in-one mOTUs_profiler mash dist mash paste mash screen mash sketch megahit contig2fastg metaMDBG assemble (ASM) metaMDBG graph (GFA) metagenomeSeq Normalization profile staramr sylph profile sylph query

Alevin AnnData Operations Build count matrix CITE-seq-Count Cluster Inspection using RaceID Clustering using RaceID Combine multiple 1D Models Combine multiple 2D Models Construct Expression Set Object Decoupler pseudo-bulk Droplet barcode rank plot DropletUtils DropletUtils Read10x DropletUtils emptyDrops EBI SCXA Data Retrieval Export AnnData GTF2GeneList Import Anndata Initial processing using RaceID Inspect AnnData Inspect Expression Set Object Lineage Branch Analysis using StemID Lineage computation using StemID Loom operations Manipulate AnnData Manipulate Expression Set Object MuSiC Compare MuSiC Deconvolution SCEasy Converter SCEasy convert Scanpy ComputeGraph Scanpy DPT Scanpy DiffusionMap Scanpy FilterCells Scanpy FilterGenes Scanpy FindCluster Scanpy FindMarkers Scanpy FindVariableGenes Scanpy Harmony Scanpy Inspect and manipulate Scanpy NormaliseData Scanpy PAGA Scanpy ParameterIterator Scanpy PlotEmbed Scanpy PlotTrajectory Scanpy Read10x Scanpy RegressOut Scanpy RunFDG Scanpy RunPCA Scanpy RunTSNE Scanpy RunUMAP Scanpy ScaleData Scanpy cluster, embed Scanpy filter Scanpy normalize Scanpy plot Scanpy remove confounders Seurat Create Seurat Data Management Seurat Find Clusters Seurat Integrate Seurat Preprocessing Seurat Run Dimensional Reduction Seurat Visualize Sinto barcode Sinto fragments SnapATAC2 Clustering SnapATAC2 Plotting SnapATAC2 Preprocessing SnapATAC2 peaks and motif baredSC 1d baredSC 2d salmonKallistoMtxTo10x scATAC-seq Preprocessing velocyto CLI

Convert a 10X BAM file to FASTQ Scater read 10x data scran_normalize

Adapt an elastic transformation Add or remove noise Add shadow effect Adjust threshold Align two images Analyze and visualize spatial multi-omics data Analyze particles Analyze skeleton Apply a morphological operation Apply anisotropic diffusion Apply elastic transformation Apply raw transformation Apply ridge filter Apply standard image filter Background subtraction Clip image intensities Colocalization ColorToGray Colorize label map Compare elastic and raw deformation Compare opposite elastic deformations Compare two raw deformations Compose a raw and an elastic transformation Compose two elastic transformations Compose two raw transformations Compute Voronoi tessellation Compute image features Compute image orientation Compute image segmentation and object detection performance measures Concatenate images Convert DICOM to TIFF Convert McMicro Output to Anndata Convert binary image to EDM Convert binary image to label map Convert binary image to points (center of masses) Convert binary image to points (point coordinates) Convert coordinates to label map Convert elastic transformation to raw Convert image format Convert label map to binary image Convert label map to points (center of masses) Convert point coordinates to binary image Convert single-channel to multi-channel image Convert to OME-Zarr Convert to binary ConvertObjectsToImage Count objects in label map Create new image Create spatial scatterplot Crop image DisplayDataOnImage Download IDR/OMERO Enhance contrast EnhanceOrSuppressFeatures Evaluate segmentation Export DICOM metadata ExportToSpreadsheet Extract image features Extract top view from whole-slide image FTP Link for Bioimage Archive Filter label map by rules Find datasets with similar ISCC-CODEs Find edges Find maxima Generate ISCC-CODE GrayToColor IdentifyPrimaryObjects ImageMath Landmark Registration Local Threshold MaskImage MeasureGranularity MeasureImageAreaOccupied MeasureImageIntensity MeasureImageQuality MeasureObjectIntensity MeasureObjectSizeShape MeasureTexture Merge neighbors in label map OMERO Dataset to Plate OMERO IDs OMERO Image Import OMERO Metadata Import OMERO ROI Import OMERO get IDs OMERO get Object Operate on pixels Overlay Overlay Segmentation Mask Overlay images OverlayOutlines Perform 2-D spot detection Perform affine image registration (intensity-based) Perform color deconvolution or transformation Perform curve fitting Perform histogram equalization Perform linking in time series (nearest neighbors) Perform projective transformation of an image Perform projective transformation of point coordinates Perform segmentation in densely packed 3-D volumetric images Perform segmentation using deformable shape models Perform segmentation using region-based fitting of overlapping ellipses Perform segmentation using watershed transformation Permutate image axes Process images using arithmetic expressions RelateObjects Remove image background Rename OME-TIFF channels Render 3-D image data Run CellProfiler pipeline Run CellProfiler pipeline SaveImages Scale image Sharpen Show image info Single Cell Phenotyping Skeletonize Smooth image Spatial plotting functions Split image along axes Split label map using morphological operators Split objects Starting Modules Switch axis coordinates Threshold image Tile TrackObjects Verify ISCC-CODE Visualize detections Vitessce

Colabfold Alphafold Colabfold MSA CustomProDB DecoyDatabase EncyclopeDIA Quantify FalseDiscoveryRate FastaCLI FeatureFinderMultiplex FragPipe - Academic Research and Education User License (Non-Commercial) FragPipe Manifest Generator IDMapper Identification Parameters KSTAR Activity Prediction MSGFPlusAdapter MSstats MSstatsTMT MaxQuant MaxQuant (using mqpar.xml) MetaNovo MetaProSIP PepPointer PepQuery PepQuery2 PepQuery2 Show Sets PepQuery2 index Peptide Genomic Coordinate Peptide Shaker PeptideIndexer Reactome Analysis Reactome GSA Analysis Search GUI SearchToLib Validate FASTA Database eggNOG Mapper eggNOG Mapper eggNOG Mapper

CAMERA.annotate Check Format ID choice Intensity Check MFAssignR FindRecalSeries MFAssignR HistNoise MFAssignR IsoFiltR MFAssignR KMDNoise MFAssignR MFAssign MFAssignR MFAssignCHO MFAssignR Recal MFAssignR RecalList MFAssignR SNplot MSnbase readMSData RAMClustR RAMClustR define experiment RIAssigner WaveICA matchMS similarity matchms filtering matchms scores formatter metaMS.runGC msconvert table rename column xcms adjustRtime (retcor) xcms fillChromPeaks (fillPeaks) xcms findChromPeaks (xcmsSet) xcms findChromPeaks Merger xcms get a sampleMetadata file xcms groupChromPeaks (group) xcms plot chromatogram xcms process history

‘FeatureStein’ fragment overlay scoring APoc Add hydrogen atoms Add hydrogen atoms Adding New Topology Information Alchemical Analysis Align structures and compute relative RMSDs Alphafold 2 Angle Analysis AnteChamber Build tLEaP Butina Cluster Butina Cluster Matrix Calculate molecular descriptors Calculate plane of best fit for molecules Calculate the box parameters using RDKit ChEMBL structure pipeline ChEMBL structure pipeline Change Title Change title Cluster ligands using SuCOS Compound Convert Compound Search Compound conversion Compound search Compute physico-chemical properties Compute physico-chemical properties Conformer calculation Constrained conformer generation Convert Amber topology and coordinate files to GROMACS format Convert Parameters Convert Qiskit’s XYZ files to Cosine Content Create Frankenstein ligand Create GROMACS index files Create GROMACS position restraints files DCCM analysis Descriptors Determine distance to defined points Dihedral Analysis Distance Analysis Drug-likeness End-to-End Analysis Enumerate changes Extract RMSD distance matrix data Extract clusters of MD trajectories Extract energy components with GROMACS Extract values from an SD-file Extracting Topology Information Filter Filter GROMACS RMSD calculation GROMACS RMSF calculation GROMACS Radius of Gyration GROMACS copy file GROMACS energy minimization GROMACS initial setup GROMACS production simulation GROMACS simulation GROMACS solvation and adding ions GROMACS structure configuration Generate MD topologies for small molecules Generate conformers Get PDB file Get PDB file Hierarchical clustering Hydrogen Bond Analysis Hydrogen Bond Analysis using VMD JMol Editor MDS Scatter Plot MDTraj file converter MMPBSA/MMGBSA Max SuCOS score Merge GROMACS topologies Modify/convert GROMACS trajectories Molecule recognition Molecule to fingerprint Multi Compound Search Multi Compound Search Natural Product likeness calculator NxN clustering Online data Online data Open 3D Align Open Molecule Generator OpenDUck chunk OpenPepXL PACKMOL PCA PCA visualization PULCHRA recontruction of all atom proteins PaDEL descriptor ParmChk2 Pharmacophore Pharmacophore alignment Pick Prepare ligand Prepare ligands for docking Prepare receptor PubChem Assay Downloader PubChem Assay Downloader PubChem Download PubChem Download QCxMS get results QCxMS neutral run QCxMS production run RDConf: Low-energy ligand conformer search RDF Analysis RMSD Analysis RMSF Analysis Ramachandran Analysis Ramachandran Plots Reaction SMARTS filter Reaction maker Remove counterions and fragments Remove counterions and fragments Remove duplicated molecules Remove duplicated molecules Remove protonation state Remove protonation state Remove small molecules Remove small molecules Run OpenDUck SDF sort and filter SDF to Fingerprint Score docked poses using SuCOS Screen Search ChEMBL database Similarity search Slice MD trajectories Spectrophores search Spectrophores(TM) search: Standardize SD-files Substructure Search Substructure Search Taylor-Butina clustering Trajectory select and merge VINA Docking Visualisation Visualisation XChem TransFS pose scoring XCos dcTMD friction correction dpocket fastpca fpocket goseq rDock cavity definition rDock docking rDock docking rxDock cavity definition rxDock docking smina

pharmCAT

Cluster, embed and annotate

CTSM/FATES-EMERALD Copernicus Climate Data Store climate stripes

NetCDF xarray Coordinate Info NetCDF xarray Metadata Info NetCDF xarray Selection NetCDF xarray map plotting NetCDF xarray operations

Hicup Deduplicator Hicup Digester Hicup Filter Hicup Mapper Hicup Pipeline Hicup Truncater Hicup to juicer converter cooler csort with tabix cooler_balance cooler_cload_tabix cooler_makebins

Analyze and visualize spatial multi-omics data MCQUANT Process single-cell intensities Slice image into patches Vitessce s3segmenter

Compute biodiversity indices Compute spectral indices Map diversity Preprocess sentinel 2 data

CloudMap: Check snpEff Candidates CloudMap: EMS Variant Density Mapping CloudMap: Hawaiian Variant Mapping with WGS data CloudMap: Variant Discovery Mapping with WGS data CloudMap: in silico complementation bcftools view

Cuffcompare Cuffdiff Cufflinks Cuffmerge Cuffnorm Cuffquant Extract CuffDiff TopHat