1666 tool(s) found

Tool Description Topics Available version(s)
2D Feature Extraction Feature Extraction 3
ABRicate Mass screening of contigs for antimicrobial and virulence genes Antimicrobial resistance prediction 8
ABRicate List List all of abricate's available databases. Antimicrobial resistance prediction 8
Abundance index computation across species, sites and years 1
Abundance index computation across species, sites and years 1
ABySS de novo sequence assembler 9
Add column to an existing dataset Editing 2
Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas] 3
Add line to file writes a line of text at the begining or end of a text file. 1
Add LoFreq alignment quality scores to aligned read SAM/BAM records 3
Add or Replace Groups 3
Add protein features [neXtProt] 3
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
addstring2fashead Converts fasta file with sequences from same species and gene family to phytab format 1
Advanced Cut columns from a table (cut) 8
AEGeAn ParsEval compare two sets of gene annotations for the same sequence. Genome annotation 1
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Alevin Quantification and analysis of 3’ tagged-end single-cell sequencing data 7
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 12
Align.check Calculate the number of potentially misaligned bases 6
Align.seqs Align sequences to a template alignment 5
alignmentsieve Filter BAM/CRAM files according to specified parameters 7
alimask append modelmask line to a multiple sequence alignments 7
Alleyoop - post-processing and QC of Slamdunk analyses 5
Amova Analysis of molecular variance 5
Annotate a VCF dataset with custom filters 1
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
Annotate with DGI database info 1
Annotate with DGI database info 1
annotateMyIDs annotate a generic set of identifiers 8
Anosim Non-parametric multivariate analysis of changes in community structure 5
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 5
Arithmetic Operations on tables 2
ARTIC minion Build consensus sequence and call variants from amplicon-based nanopore sequence data 5
Associate HUMAnN2 functions with metadata 3
Augustus gene prediction for prokaryotic and eukaryotic genomes 7
Auto Threshold applies a standard thresholding algorithm to an image 3
Autocorrelation test check for temporal autocorrelation in the residuals 1
Autocorrelation test check for temporal autocorrelation in the residuals 1
Automated multiple sequence alignment with pipelign 1
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
backtranseq Back translate a protein sequence 7
BAM filter Removes reads from a BAM file based on criteria 4
BAM Index Statistics 3
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 7
BAM-to-SAM convert BAM to SAM 5
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 7
bamCompare normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them 17
bamCoverage generates a coverage bigWig file from a given BAM or CRAM file 18
BamLeftAlign indels in BAM datasets 13
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 17
banana Bending and curvature plot in B-DNA 5
Bandage Image visualize de novo assembly graphs 6
Bandage Info determine statistics of de novo assembly graphs 5
Bar chart for multiple columns 2
Barcode Splitter 4
Barplot stratified HUMAnN2 features 3
Base Coverage of all intervals Quantification 4
basil Breakpoint detection, including large insertions 1
Batch_correction Corrects intensities for signal drift and batch-effects 4
bax2bam converts PacBio basecall format (bax.h5) into BAM Conversion 2
BayeScan Detecting natural selection from population-based genetic data 1
bcftools call SNP/indel variant calling from VCF/BCF 8
bcftools cnv Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR) 9
bcftools color-chrs plugin Color shared chromosomal segments, requires phased GTs 3
bcftools concat Concatenate or combine VCF/BCF files 6
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 9
bcftools csq Haplotype aware consequence predictor 7
bcftools frameshifts plugin Annotate frameshift indels 3
bcftools merge Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file 7
bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows 9
bcftools stats Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats 7
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 10
bcftoolsView Convert, filter, subset VCF/BCF files 1
BEAM significant single- and multi-locus SNP associations in case-control studies 1
BEAST 1.7.2 Bayesian evolutionary analysis by sampling trees. 1
beautifyfasta Converts interleaved fasta to non-interleaved 1
bed to protein map genomic location of proteins for MVP 2
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 2
BedCov calculate read depth for a set of genomic intervals 5
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 17
Bin.seqs Order Sequences by OTU 5
Binary 2 Label Converts Binary to Label Image 2
biosed Replace or delete sequence sections 5
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
blockbuster detects blocks of overlapping reads using a gaussian-distribution approach 3
BlockClust efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles 2
Bowtie2 - map reads against reference genome 19
Boxplot of quality statistics 2
Braker genome annotation 1
btwisted Calculates the twisting in a B-DNA sequence 5
Build custom track for UCSC genome browser 3
Build Deep learning Batch Training Models with online data generator for Genomic/Protein sequences and images 5
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 12
Build tissue-specific expression dataset [Human Protein Atlas](no input required) 2
Busco assess genome assembly and annotation completeness 12
bwameth Fast and accurate aligner of BS-Seq reads. 6
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate a Heinz score for each node 2
Calculate metrics for classification performance 12
Calculate metrics for regression performance 11
Call and phase heterozygous SNPs 4
Call specific mutations in reads: Looks for reads with mutation at known positions and calculates frequencies and stats. 3
Call variants with LoFreq 6
CalMD recalculate MD/NM tags 5
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 9
Canonical Correlation Analysis 1
cast expand combinations of variables:values to columnar format 1
CAT add_names annotate with taxonomic names 1
CAT bins annotate with taxonomic classification 2
CAT contigs annotate with taxonomic classification 2
CAT prepare a database for CAT - Contig Annotation Tool 1
CAT summarise the number of contigs or bins assigned to each taxonomic name 1
Categorize Elements satisfying criteria 1
CCAT Control-based ChIP-seq Analysis Tool 2
CellProfiler run a CellProfiler pipeline 2
Change Case of selected columns 2
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 5
checktrans Reports STOP codons and ORF statistics of a protein 5
chicAggregateStatistic computes with a target file the to be tested regions for chicDifferentialTest 6
chicDifferentialTest computes differential interactions of viewpoints 6
chicPlotViewpoint creates plots for viewpoints 6
chicQualityControl generates an estimate of the quality of each viewpoint 6
chicSignificantInteractions computes viewpoints with the given reference points and a background model 6
chicViewpoint computes viewpoints with the given reference points and a background model. 6
chicViewpointBackgroundModel compute a background model for cHi-C / HiChIP data 5
Chimera.bellerophon Find putative chimeras using bellerophon 5
Chimera.ccode Find putative chimeras using ccode 6
Chimera.check Find putative chimeras using chimeraCheck 5
Chimera.perseus Find putative chimeras using chimeraCheck 6
Chimera.pintail Find putative chimeras using pintail 5
Chimera.slayer Find putative chimeras using slayer 5
Chimera.uchime Find putative chimeras using uchime 5
Chimera.vsearch find potential chimeric sequences using vsearch 4
chips Codon usage statistics 5
ChiRA collapse deduplicate fastq reads 17
ChiRA extract extrat the chimeras 17
ChiRA map map reads to trascriptome 17
ChiRA merge merge aligned positions 17
ChiRA qauntify quantify aligned loci to score the alignments 17
Chop.seqs Trim sequences to a specified length 6
Chromeister ultra-fast pairwise genome comparisons 4
Circos visualizes data in a circular layout Visualisation 11
Circos: Alignments to links reformats alignment files to prepare for Circos Parsing 10
Circos: bigWig to Scatter reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots Conversion 10
Circos: Bundle Links reduce numbers of links in datasets before plotting Aggregation 10
Circos: Interval to Circos Text Labels reformats interval files to prepare for Circos text labels Conversion 10
Circos: Interval to Tiles reformats interval files to prepare for Circos tile plots Conversion 10
Circos: Link Density Track reduce links to a density plot Aggregation 10
Circos: Resample 1/2D data reduce numbers of points in a dataset before plotting Aggregation 10
Circos: Stack bigWigs as Histogram reformats for use in Circos stacked histogram plots Formatting 6
Circos: Table viewer easily creates circos plots from tabular data Visualisation 10
cirdna Draws circular maps of DNA constructs 5
Classify.otu Assign sequences to taxonomy 5
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 5
Classify.tree Get a consensus taxonomy for each node on a tree 5
CleanSam perform SAM/BAM grooming 14
Clearcut Generate a tree using relaxed neighbor joining 5
Clip adapter sequences 6
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 7
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 4
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 4
Cluster Inspection using RaceID examines gene expression within clusters 5
Cluster, infer trajectories and embed with scanpy 7
Cluster.classic Assign sequences to OTUs (Dotur implementation) 5
Cluster.fragments Group sequences that are part of a larger sequence 5
Cluster.split Assign sequences to OTUs and split large matrices 5
Clustering using RaceID performs clustering, outlier detection, dimensional reduction 5
CML to InChI 3
CML to mol2 3
CML to SDF 3
codcmp Codon usage table comparison 5
codeML Detects positive selection (paml package) 3
coderet Extract CDS, mRNA and translations from feature tables 5
Codon_density To compare Ribo-seq alignments between two sets of conditions, to determine codon occupancy 1
Collapse sequences 3
Collapse Collection into single dataset in order of the collection 5
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
Collect.shared Generate collector's curves for calculators on OTUs 5
Collect.single Generate collector's curves for OTUs 7
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 3
CollectInsertSizeMetrics plots distribution of insert sizes 14
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 14
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
Column arrange by header name 2
Column Join on Collections 5
Column Regex Find And Replace 4
Combine FASTA and QUAL into FASTQ Aggregation 5
Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 2
Compare multiple VCF datasets 1
Compare two Datasets to find common or distinct rows Filtering 1
Complement intervals of a dataset Sequence coordinate conversion 5
Compound conversion - interconvert between various chemistry and molecular modeling data files 6
compseq Count composition of dimer/trimer/etc words in a sequence 5
Compute an expression on every row 9
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute Motif Frequencies in indel flanking regions 2
Compute Motif Frequencies For All Motifs motif by motif 2
Compute quality statistics for SOLiD data 1
Compute quality statistics 3
Compute sequence length 6
computeGCBias Determine the GC bias of your sequenced reads 18
computeMatrix prepares data for plotting a heatmap or a profile of given regions 17
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 11
Concatenate two BED files Aggregation 5
Concatenate FASTA alignment by species 3
Concatenate datasets tail-to-head Aggregation 1
Concatenate datasets tail-to-head (cat) 10
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
ConsensusID Computes a consensus of peptide identifications of several identification engines. 6
Control-FREEC detects copy-number changes and allelic imbalances 3
Convert delimiters to TAB 1
Convert SOLiD output to fastq 1
Convert between BIOM table formats 5
Convert BAM to ScIdx 2
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert CSV to tabular 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to fai file 1
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert from BAM to FastQ 13
Convert genome coordinates between assemblies and genomes 2
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert GFF3 to prot_table for TRANSIT 4
Convert gffCompare annotated GTF to BED for StringTie results 4
Convert GTF to BED12 1
Convert image Convert image 1
Convert Kraken data to Galaxy taxonomy representation 3
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to interval 2
Convert SAM to BAM without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 2
Convert tar to directory 2
Convert uncompressed BCF to BCF 1
Convert, Merge, Randomize BAM datasets and perform other transformations 5
ConvertObjectsToImage convert the identified objects into an image 2
CoNvex Gap-cost alignMents for Long Reads 1
Cooccurrence tests whether presence-absence patterns differ from chance 6
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 17
Correlation for numeric columns 1
Cosine Content - measure the cosine content of the PCA projection 4
Count occurrences of each record 2
Count GFF Features 2
Count Objects in labled images 1
Count.groups counts the number of sequences represented by a specific group or set of groups 5
Count.seqs (aka make.table) counts the number of sequences represented by the representative 5
Coverage of a set of intervals on second set of intervals Comparison Filtering 4
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 5
Create a BedGraph of genome coverage 3
Create a deep learning model architecture using Keras 6
Create a genus level gene families file 3
Create a histogram of genome coverage 3
Create a model to recommend tools using deep learning 3
Create assemblies with Unicycler Genome assembly 8
Create deep learning model with an optimizer, loss function and fit parameters 6
Create Frankenstein ligand for docking active site definition 3
Create InterMine Interchange Dataset 1
Create single interval as a new dataset 1
Create text file with recurring lines 8
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 5
CRISPR Studio facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect 1
CRISPResso2 1
Cross-contamination Barcode Filter for use in plate-based barcoded analyses 3
CrossMap BAM Convert genome coordinates or annotation files between genome assemblies 5
CrossMap BED Convert genome coordinates or annotation files between genome assemblies 5
CrossMap GFF Convert genome coordinates or annotation files between genome assemblies 5
CrossMap VCF Convert genome coordinates or annotation files between genome assemblies 4
CrossMap Wig Convert genome coordinates or annotation files between genome assemblies 4
CSV to Tabular 1
CTD analysis of chemicals, diseases, or genes 1
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 8
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 12
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 7
Cuffquant Precompute gene expression levels 4
cummeRbund visualize Cuffdiff output 3
cusp Create a codon usage table 5
CustomProDB Generate protein FASTAs from exosome or transcriptome data 2
Cut columns from a table Filtering 2
Cutadapt Remove adapter sequences from Fastq/Fasta Sequence editing 20
cuteSV detects long-read-based SVs 1
cutseq Removes a specified section from a sequence 5
dada2: assignTaxonomy and addSpecies Learn Error rates 6
dada2: dada Remove sequencing errors 6
dada2: filterAndTrim Filter and trim short read data 6
dada2: learnErrors Learn Error rates 6
dada2: makeSequenceTable construct a sequence table (analogous to OTU table) 6
dada2: mergePairs Merge denoised forward and reverse reads 6
dada2: plotComplexity Plot sequence complexity profile 6
dada2: plotQualityProfile plot a visual summary of the quality scores 6
dada2: removeBimeraDenovo Remove bimeras from collections of unique sequences 6
dada2: sequence counts 6
dan Calculates DNA RNA/DNA melting temperature 5
Data Fetch Query and retrieval 1
Datamash (operations on tabular data) 3
DAVID functional annotation for a list of genes 1
DCS mutations to SSCS stats: Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies 3
DCS mutations to tags/reads: Extracts all tags that carry a mutation in the duplex consensus sequence (DCS) 3
Deep learning training and evaluation conduct deep training and evaluation either implicitly or explicitly 4
Degap.seqs Remove gap characters from sequences 5
degapseq Removes gap characters from sequences 5
Delete Overlapping Indels from a chromosome indels file 1
Deletion Profile calculates the distributions of deleted nucleotides across reads 3
Delly call and genotype structural variants 4
Delly classify somatic or germline copy-number variants 2
Delly cnv discover and genotype copy-number variants 2
Delly filter somatic or germline structural variants 4
Delly long-read (lr) optimized calling and genotyping of structural variants 4
Delly merge structural variants across/within BCF/VCF file(s) 4
Delta-Filter Filters alignment (delta) file from nucmer Read mapping Sequence alignment 5
Describe samples and replicates 11
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 21
Determine_batch_correction to choose between linear, lowess and loess methods 4
Deunique.seqs Return all sequences 5
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 5
DEXSeq Determines differential exon usage from count tables 9
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 9
diapysef library generation generates spectral library for DIA analysis 1
diff analyzes two files and generates an unidiff text file with information about the differences and an optional Html report 3
Differential expression analysis using a Trinity assembly 11
Differential Translation Analysis (Step 4) Get Ribo and RNA-Seq counts with riboSeqR. Perform differential translation analysis with baySeq. 1
diffseq Find differences between nearly identical sequences 5
digest Protein proteolytic enzyme or reagent cleavage digest 5
DISCO to assemble metagenomics data using an overlap-layout-consensus (OLC) approach 2
Discriminant Analysis 12
DisplayDataOnImage produce an image with data on top of identified objects 2
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
DNAdiff Evaluate similarities/differences between two sequences Read mapping Sequence alignment 5
dotmatcher Displays a thresholded dotplot of two sequences 5
dotpath Non-overlapping wordmatch dotplot of two sequences 5
dottup Displays a wordmatch dotplot of two sequences 5
Download and Extract Reads in BAM format from NCBI SRA 22
Download and Extract Reads in FASTA/Q format from NCBI SRA 18
Download and Generate Pileup Format from NCBI SRA 9
Download run data from EBI Metagenomics database 1
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
Draw nucleotides distribution chart 4
Draw phylogeny 1
Draw quality score boxplot for SOLiD data 1
Draw quality score boxplot 4
Draw ROC plot on "Perform LDA" output 2
Draw Stacked Bar Plots for different categories and different criteria 1
dreg Regular expression search of a nucleotide sequence 7
dRep compare compare a list of genomes 2
dRep dereplicate De-replicate a list of genomes 2
DropletUtils Utilities for handling droplet-based single-cell RNA-seq data DNA barcoding Parsing 9
Du Novo: Align families of duplex sequencing reads 10
Du Novo: Check input for family content 3
Du Novo: Correct barcodes of duplex sequencing reads 11
Du Novo: Make consensus reads from duplex sequencing alignments 10
Du Novo: Make families of duplex sequencing reads 10
EBI Search to obtain search results on resources and services hosted at the EBI 2
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
EGA Download Client 1
eggNOG Mapper functional sequence annotation by orthology 7
EGSEA easy and efficient ensemble gene set testing 4
einverted Finds DNA inverted repeats 5
ENA Upload tool 7
EnhanceOrSuppressFeatures to improve subsequent identification of objects 2
Ensemble methods for classification and regression 12
Enumerate changes calculated with Dimorphite DL and RDKit 3
epestfind Finds PEST motifs as potential proteolytic cleavage sites 5
equicktandem Finds tandem repeats 5
est2genome Align EST and genomic DNA sequences 5
Estimate Library Complexity 3
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
estimateReadFiltering estimates the number of reads that would be filtered given certain criteria 6
Estimator attributes get important attributes from an estimator or scikit object 9
etandem Looks for tandem repeats in a nucleotide sequence 5
Evaluate a Fitted Model using a new batch of labeled data 6
Evaluate pairwise distances or compute affinity or kernel for sets of samples 12
EvolMAP Runs EvolMAP. 1
EvolMAP Long Runs EvolMAP for longer (bigger) jobs. 1
EvolMAP Output Species Exclude Modifies EvolMAP Output to exclude specific species. 1
EvolMAP Output to FASTA Converts EvolMAP Output file to FASTA file 1
EvolMAP Output Tool Modifies EvolMAP output 1
Exonerate pairwise sequence comparison 4
Expected temporal trend of species abundance 1
Expected temporal trend of species abundance 1
Export AnnData and loom files Interconvert AnnData and Loom formats 8
Export to GraPhlAn 2
ExportToSpreadsheet export measurements into one or more files 2
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
Extract alignment ends from SAM or BAM 3
Extract and cluster differentially expressed transcripts from a Trinity assembly 12
Extract CuffDiff tabular files from a cummeRbund database 2
Extract element identifiers of a list collection 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF blocks given a set of genomic intervals 3
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract ORF from a GenBank file 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
extractfeat Extract features from a sequence 5
extractseq Extract regions from a sequence 5
FalseDiscoveryRate Estimates the false discovery rate on peptide and protein level using decoy searches. 7
fargene Fragmented antibiotic resistance gene identifier 2
FASConcat Appends all input sequence files into one file 1
faSplit Split a FASTA file 3
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 4
Fasta nucleotide color plot 2
Fasta nucleotide color plot 1
Fasta Statistics Display summary statistics for a fasta file. 5
FASTA Width formatter 3
FASTA-to-Tabular converter 3
fasta2phylipE Convert Aligned FASTA to phylip Extended 1
FastANI fast alignment-free computation of whole-genome Average Nucleotide Identity 1
Faster Download and Extract Reads in FASTQ format from NCBI SRA 12
fastp - fast all-in-one preprocessing for FASTQ files 8
FASTQ de-interlacer on paired end reads Splitting 5
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FASTQ interlacer on paired end reads Aggregation 6
FASTQ joiner on paired end reads Aggregation 7
FASTQ Masker by quality score Sequence masking 5
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads Splitting 6
FASTQ Summary Statistics by column Sequence assembly validation 4
FASTQ to FASTA converter Conversion 5
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 6
FASTQ to Tabular converter Sequence conversion 5
FASTQ Trimmer by column Sequence trimming 5
Fastq.info Convert fastq to fasta and quality 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FASTQE visualize fastq files with emoji's 🧬😎 5
FastqToSam convert Fastq data into unaligned BAM 18
FASTTREE build maximum-likelihood phylogenetic trees Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
Feature coverage 1
Feature Selection module, including univariate filter selection methods and recursive feature elimination algorithm 12
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
FeatureFinderMultiplex Determination of peak ratios in LC-MS data 7
FEELnc FlExible Extraction of LncRNA 5
Fetch closest non-overlapping feature for every interval Filtering 3
Fetch Indels from 3-way alignments 1
Fetch taxonomic representation 2
fgsea - fast preranked gene set enrichment analysis 3
FidoAdapter Runs the protein inference engine Fido. 6
FileConverter Converts between different MS file formats. 5
FileFilter Extracts or manipulates portions of data from peak, feature or consensus-feature files. 5
FileInfo Shows basic information about the file, such as data ranges and file type. 5
FileMerger Merges several MS files into one file. 5
Filter data on any column using simple expressions Formatting 2
Filter a VCF file 1
Filter BAM datasets on a variety of attributes 5
Filter with scanpy 7
Filter by keywords and/or numerical value 4
Filter by quality Filtering 6
Filter Combined Transcripts using tracking file 1
Filter FASTQ reads by quality score and length Filtering 4
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 2
Filter Image applies a standard filter to an image 2
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter pileup on coverage and SNPs 3
Filter SAM on bitwise flag values 1
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 5
Filter segmentation Filter segmentation by rules 1
Filter sequences by length Filtering 6
Filter Tabular 5
Filter with SortMeRNA of ribosomal RNAs in metatranscriptomic data 6
Filter.seqs removes columns from alignments 5
Filter.shared remove OTUs based on various critieria 6
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
filtlong Filtering long reads by quality 3
FIMO - Scan a set of sequences for motifs 11
Find and replace text from a dataset 1
Find diagnostic hits 1
Find lowest diagnostic rank 1
Finds SNP sites from a multi-FASTA alignment file 1
Fit a BUM model with p-values 2
Fit a Pipeline, Ensemble or other models using a labeled dataset 6
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
Flagstat tabulate descriptive stats for BAM datset 8
FLAIR collapse defines high-confidence isoforms from flair-corrected reads 3
FLAIR correct corrects misaligned splice sites using genome annotations 2
FLASH adjust length of short reads 6
FlashLFQ ultrafast label-free quantification for mass-spectrometry proteomics 5
Flight curve compute the regional expected pattern of abundance 1
Flight curve compute the regional expected pattern of abundance 1
Flye assembly of long and error-prone reads Genome assembly 7
Format MetaPhlAn2 output for Krona 2
Format MetaPhlAn2 output to extract abundance at different taxonomic levels 1
FPKM Count calculates raw read count, FPM, and FPKM for each gene 5
FragGeneScan for finding (fragmented) genes in short reads 1
Frame To analyse Ribo-seq alignments for the extraction of translational ambiguities 1
freak Residue/base frequency table or plot 5
FreeBayes bayesian genetic variant detector 13
Funannotate assembly clean 4
Funannotate compare annotations 4
Funannotate functional annotation 4
Funannotate predict annotation 5
FunDO human genes associated with disease terms 2
fuzznuc Nucleic acid pattern search 6
fuzzpro Protein pattern search 5
fuzztran Protein pattern search after translation 5
g:Profiler tools for functional profiling of gene lists 1
garnier Predicts protein secondary structure 5
GATK4 Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes 7
Gblocks Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Sequence masking 3
GC Skew calculates skew over genomic sequences Nucleic acid property calculation 10
Gecko Ungapped genome comparison 3
geecee Calculates fractional GC content of nucleic acid sequences 5
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 3
GEMINI amend Amend an already loaded GEMINI database. 4
GEMINI annotate the variants in an existing GEMINI database with additional information 6
GEMINI burden perform sample-wise gene-level burden calculations 3
GEMINI database info Retrieve information about tables, columns and annotation data stored in a GEMINI database 3
GEMINI fusions Identify somatic fusion genes from a GEMINI database 4
GEMINI gene_wise Custom genotype filtering by gene 4
GEMINI inheritance pattern based identification of candidate genes 1
GEMINI interactions Find genes among variants that are interacting partners 3
GEMINI load Loading a VCF file into GEMINI 6
GEMINI lof_sieve Filter LoF variants by transcript position and type 3
GEMINI pathways Map genes and variants to KEGG pathways 4
GEMINI qc Quality control tool 4
GEMINI query Querying the GEMINI database 4
GEMINI roh Identifying runs of homozygosity 4
GEMINI set_somatic Tag somatic mutations in a GEMINI database 4
GEMINI stats Compute useful variant statistics 3
GEMINI windower Conducting analyses on genome "windows" 3
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 10
Gene Body Coverage (Bigwig) Read coverage over gene body 10
Gene length and GC content from GTF and FASTA file 4
Generalized linear models for classification and regression 11
Generate random samples with controlled size and complexity 12
Generate A Matrix for using PC and LDA 1
Generate MD topologies for small molecules using acpype 10
Generate pileup from BAM dataset 3
Generate SuperTranscripts from a Trinity assembly 6
Generation, personalization and annotation of tree for GraPhlAn 2
Generic_Filter Removes elements according to numerical or qualitative values 3
Genome annotation statistics 1
Genrich Detecting sites of genomic enrichment 3
Get flanks returns flanking region/s for every gene Sequence analysis 4
Get Microbial Data Query and retrieval 1
Get MS/MS observations in tissue/fluid [Peptide Atlas] 3
Get open reading frames (ORFs) or coding sequences (CDSs) e.g. to get peptides from ESTs 5
Get PDB file from Protein Data Bank 2
Get species occurrences data from GBIF, ALA, iNAT and others 1
Get.communitytype description 5
Get.coremicrobiome fraction of OTUs for samples or abundances 6
Get.dists selects distances from a phylip or column file 5
Get.group group names from shared or from list and group 6
Get.groups Select groups 5
Get.label label names from list, sabund, or rabund file 5
Get.lineage Picks by taxon 6
Get.mimarkspackage creates a mimarks package form with your groups 5
Get.otulabels Selects OTU labels 6
Get.otulist Get otus for each distance in a otu list 5
Get.oturep Generate a fasta with a representative sequence for each OTU 5
Get.otus Get otus containing sequences from specified groups 5
Get.rabund Get rabund from a otu list or sabund 6
Get.relabund Calculate the relative abundance of each otu 5
Get.sabund Get sabund from a otu list or rabund 5
Get.seqs Picks sequences by name 5
Get.sharedseqs Get shared sequences at each distance from list and group 5
GetFastaBed use intervals to extract sequences from a FASTA file 20
getorf Finds and extracts open reading frames (ORFs) 5
GFA to FASTA Convert Graphical Fragment Assembly files to FASTA format 4
GFF-to-BED converter Conversion 2
GffCompare compare assembled transcripts to a reference annotation 4
gffread Filters and/or converts GFF3/GTF2 records 7
Glimmer ICM builder 2
Glimmer3 Predict ORFs in prokaryotic genomes (knowlegde-based) 2
Glimmer3 Predict ORFs in prokaryotic genomes (not knowlegde-based) 2
GMAJ Multiple Alignment Viewer 1
GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] 3
GOEnrichment performs GO enrichment analysis of a set of gene products 2
goseq tests for overrepresented gene categories Gene-set enrichment analysis 10
GOSlimmer converts a set of annotation from GO to a given GOSlim version 2
GPASS significant single-SNP associations in case-control studies 1
gProfiler Convert converts between various types of namespaces 2
gProfiler GOSt performs functional enrichment analysis of gene lists Gene-set enrichment analysis 2
gProfiler Orth translates gene identifiers between organisms 2
gProfiler Random generates a gene list 2
gProfiler SNPense maps SNP rs-codes to gene names, chromosomal coordinates and variant effects 2
GraphEmbed Compute and plot a 2D embedding of a data matrix given supervised class information 1
GraPhlAn to produce graphical output of an input tree 2
GrayToColor take grayscale images and produces a color image from them 2
GROMACS energy minimization of the system prior to equilibration and production MD 7
GROMACS initial setup of topology and GRO structure file 6
GROMACS simulation for system equilibration or data collection 9
GROMACS solvation and adding ions to structure and topology files 8
GROMACS structure configuration using editconf 5
Group data by a column and perform aggregate operation on other columns. 4
Group abundances of UniRef50 gene families obtained (HUMAnN2 output) to Gene Ontology (GO) slim terms 2
GTF-to-BEDGraph converter Conversion 1
Gubbins Recombination detection in Bacteria 1
Gumbel - determine essential genes 6
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
Heatmap w ggplot 3
Heatmap.bin Generate a heatmap for OTUs 5
Heatmap.sim Generate a heatmap for pariwise similarity 5
heatmap2 4
helixturnhelix Report nucleic acid binding motifs 5
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 3
hicAdjustMatrix adjust the shape of a Hi-C matrix 5
hicAggregateContacts allow plotting of aggregated Hi-C contacts between regions specified in a file 9
hicAverageRegions sums Hi-C contacts around given reference points and computes their average. 5
hicBuildMatrix create a contact matrix 17
hicCompareMatrices normalize and compare two Hi-C contact matrices 10
hicCompartmentalization compute pairwise correlations between multiple Hi-C contact matrices 5
hicConvertFormat Convert between different file formats 6
hicCorrectMatrix run a Hi-C matrix correction algorithm 16
hicCorrelate compute pairwise correlations between multiple Hi-C contact matrices 14
hicDetectLoops searches for enriched regions 5
hicFindRestSite identify restriction enzyme sites 6
hicFindTADs identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin 15
hicInfo get information about the content of a Hi-C matrix 5
hicMergeLoops merge detected loops of different resolutions. 6
hicMergeMatrixBins merge adjacent bins from a Hi-C contact matrix to reduce its resolution 14
hicNormalize normalizes a matrix to norm range or smallest read count 6
hicPCA compute the principal components for A / B compartment analysis 11
hicPlotAverageRegions plot the average regions from hicAverageRegions 6
hicPlotDistVsCounts compute distance vs Hi-C counts plot per chromosome 14
hicPlotMatrix plot a Hi-C contact matrix heatmap 15
hicPlotSVL plots the relation of short vs long range contacts 5
hicPlotTADs plot Hi-C contact matrices heatmaps alongside other data tracks 9
hicPlotViewpoint plot interactions around a viewpoint 11
hicQuickQC get a first quality estimate of Hi-C data 6
hicSumMatrices combine Hi-C matrices of the same size 15
hicTransform transform a matrix to obs/exp, pearson and covariance matrices 11
hicValidateLocations validate detected loops with protein peaks. 5
HighResPrecursorMassCorrector Corrects the precursor mass and charge determined by the instrument software. 5
HISAT2 A fast and sensitive alignment program 18
Histogram of a numeric column 4
Histogram equalization automatic histogram equalization 1
Histogram w ggplot2 4
HMDB MS search search by masses on HMDB online LCMS bank 4
hmmalign align sequences to a profile HMM 7
hmmbuild Build a profile HMM from an input multiple alignment 8
hmmconvert convert profile file to a HMMER format 7
hmmemit sample sequence(s) from a profile HMM 7
hmmfetch retrieve profile HMM(s) from a file 7
hmmscan search sequence(s) against a profile database 8
hmmsearch search profile(s) against a sequence database 8
hmoment Hydrophobic moment calculation 5
Homova Homogeneity of molecular variance 5
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
HUMAnN2 to profile presence/absence and abundance of microbial pathways and gene families 5
HVIS visualization of genomic data with the Hilbert curve 2
Hydrogen Bond Analysis using VMD between two segments of a trajectory 1
Hyperparameter Search performs hyperparameter optimization using various SearchCVs 11
HyPhy-aBSREL adaptive Branch Site Random Effects Likelihood 24
HyPhy-BGM - Detecting coevolving sites via Bayesian graphical models 23
HyPhy-BUSTED Branch-site Unrestricted Statistical Test for Episodic Diversification 23
HyPhy-FADE : FUBAR* Approach to Directional Evolution (*Fast Unconstrained Bayesian Approximation) 22
HyPhy-FEL Fixed Effects Likelihood 22
HyPhy-FUBAR Fast Unconstrained Bayesian AppRoximation 22
HyPhy-GARD Genetic Algorithm for Recombination Detection 23
HyPhy-MEME Mixed Effects Model of Evolution 22
HyPhy-PRIME Property Informed Models of Evolution 17
HyPhy-RELAX Detect relaxed selection in a codon-based phylogenetic framework 21
HyPhy-SLAC Single Likelihood Ancestor Counting 22
HyPhy-SM2019 Partition Tree using Modified Slatkin-Maddison Test 22
iAssembler Assembly of transcriptomes. 1
ID Converter (Human, Mouse, Rat) 2
IDBA-HYBRID Iterative de Bruijn Graph Assembler for hybrid sequencing data 1
IDBA-TRAN Iterative de Bruijn Graph Assembler for transcriptome data 2
IDBA-UD Iterative de Bruijn Graph Assembler for data with highly uneven depth 2
IDConflictResolver Resolves ambiguous annotations of features with peptide identifications 5
Identify optimal scoring subnetwork using Heinz 2
IdentifyPrimaryObjects identify biological objects of interest 2
IDFilter Filters results from protein or peptide identification engines based on different criteria. 6
IDMapper Assigns protein/peptide identifications to features or consensus features. 5
IDMerger Merges several protein/peptide identification files into one file. 6
IDPosteriorErrorProbability Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 5
IDR compare ranked list of identifications 2
IDR/OMERO Download - download images from any OMERO instance using image IDs 10
IDScoreSwitcher Switches between different scores of peptide or protein hits in identification data 6
IdxStats reports stats of the BAM index file 8
IEDB MHC Binding prediction 3
iep Calculates the isoelectric point of a protein 5
IlluQC Parallel Runs IlluQC Parallel verion 1
Image Converter 3
Image Info Show Image Info 2
Image Montage 3
ImageMath perform simple mathematical operations on images 2
Import Anndata and loom from different format 8
InChI to CML 3
InChI to MOL 3
InChI to MOL2 3
InChI to SDF 3
Indicator Identify indicator "species" for nodes on a tree 5
Infer Experiment speculates how RNA-seq were configured 9
infoseq Displays some simple information about sequences 5
Initial processing using RaceID performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data 7
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 9
Insert indel qualities into a BAM file 3
Insertion Profile calculates the distribution of inserted nucleotides across reads 3
Insertion size metrics for PAIRED data 3
Inspect and manipulate with scanpy 7
Inspect AnnData object 8
InterProScan functional annotation 6
Intersect the intervals of two datasets Filtering 5
Intersect multiple VCF datasets 2
Intersect intervals find overlapping intervals in various ways 22
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 7
Iris Refine insertion sequences 2
isochore Plots isochores in large DNA sequences 5
ivar consensus Call consensus from aligned BAM file 5
ivar filtervariants Filter variants across replicates or multiple samples aligned using the same reference 5
ivar getmasked Detect primer mismatches and get primer indices for the amplicon to be masked 4
ivar removereads Remove reads from trimmed BAM file 8
ivar trim Trim reads in aligned BAM 9
ivar variants Call variants from aligned BAM file 6
IWTomics Load Smooth and Plot 1
IWTomics Plot with Threshold on Test Scale 1
IWTomics Test and Plot 1
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 8
JasmineSV Merge structural variants across samples 2
JBrowse genome browser Map drawing Sequence visualisation 31
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance Conversion 30
Je-Demultiplex demultiplexes fastq files 2
JModelTest 1.0 JModelTest description here. 1
Join the intervals of two datasets side-by-side Aggregation 4
Join HUMAnN2 generated tables 4
Join two files 11
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
Join two files on column allowing a small difference 2
JQ process JSON 1
Junction Annotation compares detected splice junctions to reference gene model 9
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 9
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 6
Kallisto quant - quantify abundances of RNA-Seq transcripts 8
Kc-Align 10
Kernel Canonical Correlation Analysis 2
Kernel Principal Component Analysis 2
khmer: Abundance Distribution Calculate abundance distribution of k-mers using pre-made k-mer countgraphs 4
khmer: Abundance Distribution (all-in-one) Calculate abundance distribution of k-mers 4
khmer: Count Median Count the median/avg k-mer abundance for each sequence 4
khmer: Extract partitions Separate sequences that are annotated with partitions into grouped files 4
khmer: Filter reads by minimal k-mer abundance 4
khmer: Filter reads below k-mer abundance of 50 4
khmer: Normalize By Median Filter reads using digital normalization via k-mer abundances Sequence file editing Sequence word comparison 5
khmer: Sequence partition all-in-one Load, partition, and annotate sequences 4
Kmer To calculate the proportion and phasing of each kmer 1
KOBAS Annotate KEGG Orthology Based Annotation System 3
KOBAS Identify KEGG Orthology Based Annotation System 3
KofamScan gene function annotation based on KEGG orthology and HMM 2
Kraken assign taxonomic labels to sequencing reads 8
Kraken taxonomic report view report of classification for multiple samples 2
Kraken-filter filter classification by confidence score 4
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 5
Kraken-translate convert taxonomy IDs to names 5
Kraken2 assign taxonomic labels to sequencing reads 5
Krona pie chart from taxonomic profile 10
LAJ Pairwise Alignment Viewer 1
LAST-split finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). 4
LAST-train finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. 5
LASTal finds local alignments between query sequences, and reference sequences. 6
LASTdb prepares sequences for subsequent comparison and alignment using lastal. 5
LASTZ : align long sequences 7
Lastz paired reads map short paired reads against reference sequence 2
LASTZ_D : estimate substitution scores matrix 5
LAV to BED Converts a LAV formatted file to BED format 1
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
Libshuff Cramer-von Mises tests communities for the same structure 5
LightGBM - train and apply LightGBM models 3
limma Perform differential expression with limma-voom or limma-trend Differential gene expression profiling RNA-seq read count analysis 19
lindna Draws linear maps of DNA constructs 5
Line/Word/Character count of a dataset 1
Lineage Branch Analysis using StemID inspects branches of a lineage tree 5
Lineage computation using StemID generates lineage from prior clustering 5
Linear regression ajusted for autocorrelation in the residuals 1
List Installed SnpEff Genomes available for variant annotation with MiModD 1
List spaln parameter tables Given a query species, list the spaln settings tables that exist, from closest related species to most different 3
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
Load built-in reference data to history 1
Lofreq filter called variants posteriorly 4
Lordec is a set a programs for correcting sequencing errors in PacBio reads 5
LotuS2 fast OTU processing pipeline 6
LPS LASSO-Patternsearch algorithm 1
LUMPY is a probabilistic framework for structural variant discovery 2
LUMPY preprocessing extracts discordant read pairs and split-read alignments from a BAM dataset 2
Machine Learning Visualization Extension includes several types of plotting for machine learning 6
MACS Model-based Analysis of ChIP-Seq 4
MACS2 bdgbroadcall Call broad peaks from bedGraph output 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files 9
MACS2 bdgpeakcall Call peaks from bedGraph output 8
MACS2 callpeak Call peaks from alignment results 11
MACS2 filterdup Remove duplicate reads at the same position 8
MACS2 predictd Predict 'd' or fragment size from alignment results 8
MACS2 randsample Randomly sample number or percentage of total reads 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) 8
MAF Coverage Stats Alignment coverage information 3
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
MAF-convert read MAF-format alignments and write them in another format. 4
MAFFT Multiple alignment program for amino acid or nucleotide sequences 7
mafft Multiple Sequence Alignment 2
MAFFT add Align a sequence,alignment or fragments to an existing alignment. 4
MAGeCK count - collect sgRNA read counts from read mapping files 7
MAGeCK GSEA - a fast implementation of Gene Set Enrichment Analysis 3
MAGeCK mle - perform maximum-likelihood estimation of gene essentiality scores 4
MAGeCK pathway - given a ranked gene list, test whether one pathway is enriched 3
MAGeCKs test - given a table of read counts, perform the sgRNA and gene ranking 4
Make Design Assign groups to Sets 5
Make strain profiles 3
Make.biom Make biom files from a shared file 5
Make.contigs Aligns paired forward and reverse fastq files to contigs as fasta and quality 6
Make.fastq Convert fasta and quality to fastq 6
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 6
Make.lookup allows you to create custom lookup files for use with shhh.flows 5
Make.shared Make a shared file from a list and a group 5
Make.sra creates the necessary files for a NCBI submission 5
Maker genome annotation pipeline 9
MALDIquant peak detection Peak detection, binning and filtering for mass-spectrometry imaging data 7
MALDIquant preprocessing Preprocessing of mass-spectrometry imaging data 4
Manipulate AnnData object 8
Manipulate FASTQ reads on various attributes Sequence conversion 4
Manipulate loom object Add layers, or row/column attributes to a loom file 6
Mantel Mantel correlation coefficient between two matrices. 5
Map annotation ids on a Maker annotation 6
Map with BFAST 1
Map with Bowtie for Illumina 7
Map with Bowtie for SOLiD 1
Map with BWA - map short reads (< 100 bp) against reference genome 11
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 13
Map with KMA 2
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences Sequence alignment 18
Map with Mosaik 1
Map with PerM for SOLiD and Illumina 1
MapBed apply a function to a column for each overlapping interval 21
Mapper for long, error-prone reads, like Nanopore ONT and PacBio 1
Mark Duplicate reads 3
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 15
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 14
marscan Finds MAR/SAR sites in nucleic sequences 5
mash screen determines how well query sequences are contained within a pool of sequences 3
mash sketch Create a reduced representation of a sequence or set of sequences, based on min-hashes 1
maSigPro Significant Gene Expression Profile Differences in Time Course Gene Expression Data 5
maskfeat Mask off features of a sequence 5
MaskImage hide portions of an image based on previously identified objects 2
maskseq Mask off regions of a sequence 5
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
matcher Finds the best local alignments between two sequences 5
Max SuCOS score - determine maximum SuCOS score of ligands against clustered fragment hits 7
MaxBin2 clusters metagenomic contigs into bins 3
MaxQuant 12
MaxQuant (using mqpar.xml) 4
MDTraj file converter - interconvert between MD trajectory file formats. 5
MeanQualityByCycle chart distribution of base qualities 14
MeasureGranularity output spectra of size measurements of the textures 2
MeasureImageAreaOccupied measure the area in an image occupied by objects 2
MeasureImageIntensity measure several intensity features across an entire image 2
MeasureImageQuality measure features that indicate image quality 2
MeasureObjectIntensity measure several intensity features for identified objects 2
MeasureObjectSizeShape measure area and shape features of identified objects 2
MeasureTexture quantify the roughness and smoothness of the textures 2
medaka consensus pipeline Assembly polishing via neural networks 9
medaka consensus tool Assembly polishing via neural networks 9
medaka variant pipeline via neural networks 8
medaka variant tool Probability decoding 12
Megablast compare short reads against htgs, nt, and wgs databases 2
MEGAHIT for metagenomics assembly 7
megamerger Merge two large overlapping nucleic acid sequences 5
melt collapse combinations of variables:values to single lines 1
MEME - Multiple EM for Motif Elicitation 9
MEME psp-gen - perform discriminative motif discovery 5
MEME-ChIP - motif discovery, enrichment analysis and clustering on large nucleotide datasets 3
Merge the overlapping intervals of a dataset Sequence merging 4
Merge multiple VCF datasets 2
Merge BAM Files merges BAM files together 3
Merge BedGraph files 3
Merge Columns together 4
Merge GROMACS topologies and GRO files 8
Merge.files Merge data 5
Merge.groups Merge groups in a shared file 5
Merge.sfffiles Merge SFF files 5
Merge.taxsummary Merge tax.summary files 6
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
merger Merge two overlapping nucleic acid sequences 5
MergeSamFiles merges multiple SAM/BAM datasets into one 14
MetaEuk Easy Predict High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 3
Metagene Analysis (Step 3) Metagene analysis using riboSeqR. 1
metagenomeSeq Normalization Cumulative sum scaling 1
MetaPhlAn2 to profile the composition of microbial communities 2
metaQuantome: create samples file by specifying the experiment's groups and associated column names 6
metaQuantome: database download the GO, EC, and NCBI databases 6
metaQuantome: expand a set of functional or taxonomy annotations 6
metaQuantome: filter for quality, redundancy, and sample coverage 6
metaQuantome: stat differential analysis of functional expression and taxonomic abundance 6
metaQuantome: visualize taxonomic analysis, functional analysis, and function-taxonomy analysis results 6
metaSPAdes assembler for metagenomics datasets 9
Metastats generate principle components plot data 5
MethylDackel A tool for processing bisulfite sequencing alignments Gene methylation analysis 7
metilene calling differentially methylated regions from bisulfite sequencing data 5
MiGMAP mapper for full-length T- and B-cell repertoire sequencing 5
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 5
MiModD Convert converts sequence data into different formats 2
MiModD Coverage Statistics calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool 2
MiModD Deletion Calling (for PE data) predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes 2
MiModD Extract Variant Sites from a BCF file 2
MiModD File Information provides summary reports for supported sequence data formats. 3
MiModD NacreousMap maps phenotypically selected variants by multi-variant linkage analysis 3
MiModD Rebase Sites from a VCF file 3
MiModD Reheader takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file 2
MiModD Report Variants in a human-friendly format that simplifies data exploration 3
MiModD Run Annotation writes run metadata in SAM format for attaching it to sequenced reads data 2
MiModD Sort takes a SAM/BAM dataset and generates a coordinate/name-sorted copy 2
MiModD Variant Annotation with functional effects on genes and transcripts 1
MiModD Variant Calling generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it 2
MiModD VCF Filter extracts lines from a vcf variant file based on field-specific filters 3
MINE - Maximal Information-based Nonparametric Exploration 2
Minia Short-read assembler based on a de Bruijn graph 3
miniasm Ultrafast de novo assembly for long noisy reads 7
Mismatch Profile calculates the distribution of mismatches across reads 3
MITOS de-novo annotation of metazoan mitochondrial genomes 2
MITOS2 de-novo annotation of metazoan mitochondrial genomes 2
MiXCR Analyze immuno clonotyes from sequence data 1
MLST Scans genomes against PubMLST schemes. 3
MLST List Lists available schemes for the MLST tool. 3
MOABS MOdel based Analysis of Bisulfite Sequencing data 2
Model Prediction predicts on new data using a preffited model 7
Model temporal trend with a simple linear regression 1
Model temporal trend with a simple linear regression 1
Model Validation includes cross_validate, cross_val_predict, learning_curve, and more 11
MOL to CML 3
MOL to MOL2 3
MOL2 to CML 3
MOL2 to InChI 3
MOL2 to MOL 3
MOL2 to SDF 3
Molecules to Fingerprints with different fingerprint types 5
MrBayes with options and commands 2
MSABOOT Output PHYLIP file with bootstrapped multiple sequence alignment data 3
msbar Mutate sequence beyond all recognition 5
msconvert Convert and filter a mass spec peak list 5
MSGFPlusAdapter MS/MS database search using MS-GF+. 6
MSI classification spatial classification of mass spectrometry imaging data 10
MSI combine combine several mass spectrometry imaging datasets into one 11
MSI data exporter exports imzML and Analyze7.5 to tabular files 7
MSI filtering tool for filtering mass spectrometry imaging data 8
MSI mz images mass spectrometry imaging m/z heatmaps 8
MSI plot spectra mass spectrometry imaging mass spectra plots 10
MSI preprocessing mass spectrometry imaging preprocessing 11
MSI Qualitycontrol mass spectrometry imaging QC 11
MSI segmentation mass spectrometry imaging spatial clustering 8
MSnbase readMSData Imports mass-spectrometry data files 3
MSstats statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry 4
Multi-Join (combine multiple files) 9
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 18
multiBigwigSummary calculates average scores for a list of two or more bigwig files 18
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 17
Mummer Align two or more sequences Read mapping Sequence alignment 5
Mummerplot Generate 2-D dotplot of aligned sequences Read mapping Sequence alignment 5
Mutate Codons with SNPs 1
mview View multiple sequence alignment in html 1
mz to sqlite Extract mzIdentML and associated proteomics datasets into a SQLite DB 5
Naive Variant Caller (NVC) - tabulate variable sites from BAM datasets 5
NanoComporeDB Process SampComp results database 3
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 5
Nanopolish eventalign - Align nanopore events to reference k-mers 3
Nanopolish methylation - Classify nucleotides as methylated or not. 3
Nanopolish polyA - Estimate the length of the poly-A tail on direct RNA reads. 3
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 3
NanopolishComp: EventalignCollapse by kmers rather than by event 2
NanopolishComp: FreqMethCalculate calculates methylation frequency at genomic CpG sites 1
NCBI Accession Download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 16
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 13
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 16
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 14
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 17
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 12
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 13
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 18
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
Nearest Neighbors Classification 11
needle Needleman-Wunsch global alignment 5
newcpgreport Report CpG rich areas 5
newcpgseek Reports CpG rich region 5
Newick Display visualize a phylogenetic tree Phylogenetic tree visualisation 2
newseq Type in a short new sequence 5
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 8
nhmmscan search DNA sequence(s) against a DNA profile database 8
NJst Estimate species tree with NJst from table of tree names and newick trees 1
Nmds generate non-metric multidimensional scaling data 6
Nonpareil to estimate average coverage and generate Nonpareil curves 1
noreturn Removes carriage return from ASCII files 5
Normalize with scanpy 7
Normalize combined meta'omic sequencing data 3
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 14
notseq Exclude a set of sequences and write out the remaining ones 5
NOVOplasty de novo assembler for short circular genomes 3
nthseq Writes one sequence from a multiple set of sequences 5
NucBed profile the nucleotide content of intervals in a FASTA file 21
Nucleotide subsequence search providing regions in BED format 2
Nucmer Align two or more sequences Read mapping Sequence alignment 5
Numeric Clustering 12
NxN Clustering of molecular fingerprints 5
ococo consensus caller on SAM/BAM 1
octanol Displays protein hydropathy 5
oddcomp Find protein sequence regions with a biased composition 5
odgi build construct a dynamic succinct variation graph 1
odgi viz variation graph visualizations 1
Online data fetching ... 2
ont_fast5_api: Compress multi read file(s) 2
ont_fast5_api: Multi to single read file(s) 2
ont_fast5_api: Single to multi read file(s) 2
ont_fast5_api: Subset of multi read file(s) 3
OrthoFinder finds orthogroups in a set of proteomes 7
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
Overlay Segmentation Mask Overlay Segmentation Mask 1
Owler fast, trimmed overlap pipeline without aligning 1
Paired Read Mate Fixer for paired data 3
Paired-end histogram of insert size frequency 1
Pairwise intersection and heatmap for genomic intervals 2
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
palindrome Looks for inverted repeats in a nucleotide sequence 5
Pangolin Phylogenetic Assignment of Outbreak Lineages 15
Parallel Coordinates Plot of tabular data 3
Parse blast XML output 2
Parse.list Generate a List file for each group 5
Parsimony Describes whether two or more communities have the same structure 5
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 12
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
pasteseq Insert one sequence into another 5
Pathview for pathway based data integration and visualization 1
patmatdb Search a protein sequence with a motif 5
Pca Principal Coordinate Analysis for a shared file 6
PCA - principal component analysis using Bio3D 2
PCA plot w ggplot2 4
PCA visualization - generate trajectories of principal components of atomic motion 2
Pcoa Principal Coordinate Analysis for a distance matrix 5
Pcr.seqs Trim sequences 6
PDAUG Add Class Label Add class label to the training data set 1
PDAUG Basic Plots Basic Plots 1
PDAUG Fisher's Plot Analyze peptide sequence data based on feature spaces 1
PDAUG Merge Dataframes Merge two data frames 1
PDAUG ML Models Machine learning modeling 1
PDAUG Peptide Data Access Fetch peptide data from inbuild datasets and public databases 1
PDAUG Peptide Sequence Analysis Peptide sequence analysis 1
PDAUG Sequence Property Based Descriptors Calculates sequence based descriptors of the peptide sequences 1
PDAUG TSVtoFASTA Converts tabular peptide sequence data into fasta format 1
PDpairs Pairwise distance between taxa in a phylogenetic tree 1
PEAKachu Calls Peaks in CLIP data 3
PeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 4
Pear Paired-End read merger 4
pepcoil Predicts coiled coil regions 5
pepinfo Plots simple amino acid properties in parallel 5
pepnet Displays proteins as a helical net 5
PepPointer classify genomic location of peptides 1
pepstats Protein statistics 5
Peptide Genomic Coordinate Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB 2
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 19
PeptideIndexer Refreshes the protein references for all peptide hits. 6
pepwheel Shows protein sequences as helices 5
pepwindow Displays protein hydropathy 5
pepwindowall Displays protein hydropathy of a set of sequences 5
Perform Best-subsets Regression 2
Perform LDA Linear Discriminant Analysis 2
phmmer search a protein sequence against a protein database (BLASTP-like) 8
PhyKit function to calculate a tree-based estimation of the evolutionary rate of a gene. 1
PhyKit function to calculate Robinson-Foulds (RF) distance between two trees. 1
PhyKit function to calculate summary statistics among patristic distances in a phylogeny 1
PhyKit function to calculate the average pairwise identity among sequences. 1
PhyKit function to calculate the number and percentage of parismony informative sites in an alignment. 1
PhyKit function to calculate treeness/RCV for a given alignment and tree. 1
PhyKit function to create a concatenated alignment file. This function is used to help in the construction of multi-locus data matrices. 1
PhyKit function to prune tips from a phylogeny. 1
PhyKit function to root phylogeny using user-specified taxa. 1
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phylobayes Runs phylobayes 1
Phylocatenator Produces concatenated sequence file from phytab file of aligned sequences 1
Phylomatic Run Phylomatic 1
Phylotype Assign sequences to OTUs based on taxonomy 5
PhyML Phylogeny software based on the maximum-likelihood method. Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
Phyogenetic reconstruction with RaXML - Maximum Likelihood based inference of large phylogenetic trees 4
phytab aliscorecut aliscorecut :: Runs Aliscore then Alicut on an aligned sequence from phytab Muscle. 1
phytab clearcut clearcut: Generate Neighbor Joining phylogeny. Input can be fasta or phytab format. 1
phytab HMMBUILD hmmbuild :: profile HMM construction from multiple sequence alignments in phytab format. 1
PHYTAB HMMSEARCH hmmsearch :: search profile(s) against a sequence database. Produces a phytab output. 1
phytab LB pruner LB_pruner: Identify genes on very long branches. 1
PHYTAB MUSCLE MUSCLE: Multiple sequence alignment. Input can be fasta or phytab format. 1
PHYTAB prank prank: Multiple sequence alignment. Input can be fasta or phytab format. 1
Phytab RaXML Phytab RaXML - RaXML for phytab format 1
Phytab RaXML pars Phytab RaXML - RaXML for phytab format 1
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 4
Pileup-to-Interval condenses pileup format into ranges of bases 4
pilon An automated genome assembly improvement and variant detection tool 2
Pipeline Builder an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers 11
place_fossils Maximum Likelihood Analysis 1
PlasFlow Prediction of plasmid sequences in metagenomic contigs 1
plink 6
Plot with scanpy 8
Plot abundance with trend line 1
Plot abundance with trend line 1
Plot actual vs predicted curves and residual plots of tabular data 1
Plot confusion matrix, precision, recall and ROC and AUC curves of tabular data 2
Plot Ribosome Profile (Step 4) Plot Ribosome profile using riboSeqR. 1
plotcon Plot quality of conservation of a sequence alignment 5
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 17
plotCoverage assesses the sequencing depth of BAM files 17
plotDEXSeq Visualization of the per gene DEXSeq results 4
plotEnrichment plots read/fragment coverage over sets of regions 13
plotFingerprint plots profiles of BAM files; useful for assesing ChIP signal strength 18
plotHeatmap creates a heatmap for score distributions across genomic regions 18
plotorf Plot potential open reading frames 5
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 17
plotProfile creates a profile plot for score distributions across genomic regions 17
Plotting tool for multiple series and graph types 5
Poisson two-sample test 1
polydot Displays all-against-all dotplots of a set of sequences 5
Porechop adapter trimmer for Oxford Nanopore reads 3
Pre.cluster Remove sequences due to pyrosequencing errors 5
preg Regular expression search of a protein sequence 7
Prepare riboSeqR input (Step 1) Prepare alignment file (SAM format, Ribo-Seq or RNA-Seq alignments) for riboSeqR analysis. 1
Preprocess raw feature vectors into standardized datasets 12
prettyplot Displays aligned sequences, with colouring and boxing 5
prettyseq Output sequence with translated ranges 5
Primer.design identify sequence fragments that are specific to particular OTUs 5
primersearch Searches DNA sequences for matches with primer pairs 5
Principal Component Analysis 1
Principal component analysis with scikit-learn 3
PRINSEQ to process quality of sequences 5
Profile Annotations for a set of genomic intervals 1
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
Promoter 2.0 Find eukaryotic PolII promoters in DNA sequences 4
Protein Database Downloader 4
Proteinortho detects orthologous proteins/genes within different species 4
Proteinortho grab proteins finds genes/proteins in a given fasta file 4
Proteinortho summary summaries the orthology-pairs/RBH files 4
prottest Selection of best-fit models of protein evolution. 1
Prune_taxa Pruning taxa from a tree or multiple trees 1
psortb Determines sub-cellular localisation of bacterial/archaeal protein sequences 4
PubChem Assay Downloader as canonical SMILES 3
PubChem Download as canonical SMILES 3
pyGenomeTracks plot genomic data tracks 10
PyProphet export Export tabular files, optional swath2stats export 2
PyProphet merge Merge multiple osw files 1
PyProphet peptide Peptide error-rate estimation 1
PyProphet protein Protein error-rate estimation 1
PyProphet score Error-rate estimation for MS1, MS2 and transition-level data 3
QualiMap BamQC 5
QualiMap Counts QC 2
QualiMap Multi-Sample BamQC 2
QualiMap RNA-Seq QC 3
Quality format converter (ASCII-Numeric) 3
Quality Metrics Metrics and graphics to check the quality of the data 2
QualityScoreDistribution chart quality score distribution 14
Quast Genome assembly Quality 11
Query Reactome pathway database 4
Query Tabular using sqlite sql 8
Racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 6
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
RAxML read placement RAxML read placement - Produces a labeled tree from RAxML. 1
raxml_pars Use RAxML to calculate a phylogeny with Parsimony 1
RCAS - RNA Centric Annotation System 2
rDock cavity definition - generate the active site definition needed for rDock docking 2
rDock docking - perform protein-ligand docking with rDock 6
Re-align with SRMA 1
Read Distribution calculates how mapped reads were distributed over genome feature 9
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 7
Read GC determines GC% and read count 7
Read NVC to check the nucleotide composition bias 7
Read Quality determines Phred quality score 7
Realign reads with LoFreq viterbi 5
Rebase GFF3 features against parent features 2
Reduce a HUMAnN2 generated table 4
Regex Find And Replace 3
Regex Replace Regular Expression replacement using the Python re module 1
Regroup a HUMAnN2 generated table by features 4
Reheader copy SAM/BAM header between datasets 4
RelateObjects assign relationships parent-children between objects 2
Remove beginning of a file 1
Remove columns by heading 1
Remove confounders with scanpy 7
Remove sequencing artifacts 5
Remove Unwanted Variation from RNA-seq data 4
Remove.dists Removes distances from a phylip or column file 6
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 5
Remove.lineage Picks by taxon 5
Remove.otulabels Removes OTU labels 6
Remove.otus Removes OTUs from various file formats 5
Remove.rare Remove rare OTUs 5
Remove.seqs Remove sequences by name 6
Rename features of a HUMAnN2 generated table 4
Rename sequences 5
Renormalize a HUMAnN2 generated table 4
ReorderSam reorder reads to match ordering in reference sequences 17
RepeatMasker screen DNA sequences for interspersed repeats and low complexity regions Repeat sequence analysis 9
Replace parts of text 11
Replace column by values which are defined in a convert file 2
Replace Text in a specific column 11
Replace Text in entire line 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Resize coordinate window of GFF data 3
Reverse columns in a tabular file 3
Reverse Complement a MAF file 1
Reverse-Complement 5
Reverse.seqs Reverse complement the sequences 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
revseq Reverse and complement a sequence 5
RmDup remove PCR duplicates 5
RMSD Analysis using Bio3D 2
RMSF Analysis using Bio3D 2
RNA fragment size calculates the fragment size for each gene/transcript 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 17
RNA STARSolo mapping, demultiplexing and gene quantification for single cell RNA-seq Sequence alignment 7
RNA/DNA converter 5
rnaQUAST A Quality Assessment Tool for De Novo Transcriptome Assemblies 3
RNASeq samples quality check for transcript quantification 11
rnaSPAdes de novo transcriptome assembler 10
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 8
Rolling window over a dataframe (e.g. for data smoothing) 1
RPKM Count calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 4
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 10
rtsne 1
RXLR Motifs Find RXLR Effectors of Plant Pathogenic Oomycetes 4
Sailfish transcript quantification from RNA-seq data 4
Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads 11
Salmon quantmerge Merge multiple quantification results into a single file 4
Salmonella Subtyping 2
SALSA scaffold long read assemblies with Hi-C 4
SAM-to-BAM convert SAM to BAM 8
SAM/BAM Alignment Summary Metrics 2
SAM/BAM GC Bias Metrics 2
SAM/BAM Hybrid Selection Metrics for targeted resequencing data 3
SampComp to compare Nanopolished datasets 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 18
Samtools depth compute the depth at each position or region 3
Samtools fastx extract FASTA or FASTQ from alignment files 2
Samtools fixmate fill mate coordinates, ISIZE and mate related flags 2
Samtools markdup marks duplicate alignments 5
Samtools merge merge multiple sorted alignment files 3
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools stats generate statistics for BAM dataset 6
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
sansa annotate structural variants Genetic variation analysis 2
sarscov2formatter 3
sarscov2summary 1
SaveImages or movie files 2
Scater: Calculate QC metrics Computes QC metrics from single-cell expression matrix 4
Scater: filter SCE with user-defined parameters or PCA 5
Scater: normalize SCE Compute normalised expression values for SCE 3
Scater: PCA plot Plot cell-level reduced dimension of a normalised SCE 4
Scater: plot expression frequency Plot the frequency of expression against the mean expression level for SCE 2
Scater: plot library QC Create plots to visualise library size, feature counts and mito gene expression 4
Scater: t-SNE plot Produces a t-SNE plot of two components 3
Scatterplot of two numeric columns 4
Scatterplot with ggplot2 6
scHicAdjustMatrix clusters single-cell Hi-C interaction matrices on the raw data 2
scHicCluster clusters single-cell Hi-C interaction matrices on the raw data 2
scHicClusterCompartments clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction 2
scHicClusterMinHash clusters single-cell Hi-C interaction matrices with MinHash dimension reduction 2
scHicClusterSVL clusters single-cell Hi-C interaction matrices with svl dimension reduction 2
scHicConsensusMatrices creates per cluster one average matrix 2
scHicCorrectMatrices correct with KR algorithm single-cell Hi-C interaction matrices 2
scHicCreateBulkMatrix creates the bulk matrix out of single-cell Hi-C interaction matrices 1
scHicDemultiplex demultiplexes Nagano 2017 raw fastq files 2
scHicInfo information about a single-cell scool matrix 2
scHicMergeMatrixBins change the resolution of the scHi-C matrices 2
scHicMergeToSCool merge multiple cool files to one scool file 1
scHicNormalize normalize single-cell Hi-C interaction matrices to the same read coverage 2
scHicPlotClusterProfiles plot single-cell Hi-C interaction matrices cluster profiles 2
scHicPlotConsensusMatrices plot single-cell Hi-C interaction matrices cluster consensus matrices 2
scHicQualityControl quality control for single-cell Hi-C interaction matrices 2
scPipe - preprocessing pipeline for single cell RNA-seq 4
Screen.seqs Screen sequences 6
Scythe Scythe - A very simple adapter trimmer. 1
SDF to CML 3
SDF to Fingerprint extract fingerprints from sdf files metadata 5
SDF to InChI 3
SDF to mol2 3
SEACR for sparse enrichment analysis 1
SEACR for sparse enrichment analysis 1
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 22
Search in textfiles (grep) 10
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression Filtering 3
Select first lines from a dataset Filtering 3
Select first lines from a dataset (head) 8
Select high quality segments 2
Select last lines from a dataset 2
Select last lines from a dataset (tail) 8
Select random lines from a file 2
Send to cloud 1
Sens.spec Determine the quality of OTU assignment 6
Separate pgSnp alleles into columns 1
Seq.error assess error rates in sequencing data 5
seq2HLA HLA genotype and expression from RNA-seq 2
seqmatchall All-against-all comparison of a set of sequences 5
seqret Reads and writes sequences 5
seqtk_comp get the nucleotide composition of FASTA/Q 6
seqtk_cutN cut sequence at long N 6
seqtk_dropse drop unpaired from interleaved Paired End FASTA/Q 6
seqtk_fqchk fastq QC (base/quality summary) 6
seqtk_hety regional heterozygosity 6
seqtk_listhet extract the position of each het 6
seqtk_mergefa merge two FASTA/Q files 6
seqtk_mergepe interleave two unpaired FASTA/Q files for a paired-end file 6
seqtk_mutfa point mutate FASTA at specified positions 6
seqtk_randbase choose a random base from hets 6
seqtk_sample random subsample of fasta or fastq sequences 6
seqtk_seq common transformation of FASTA/Q 6
seqtk_subseq extract subsequences from FASTA/Q files 6
seqtk_trimfq trim FASTQ using the Phred algorithm 6
Sequence Content Trimmer trim reads based on certain bases 1
Sequence Gap Remover Removes gap in sequences 1
Sequence Logo generator for fasta (eg Clustal alignments) 2
seqwish Alignment to variation graph inducer 5
Seurat - toolkit for exploration of single-cell RNA-seq data 9
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Shasta De novo assembly of long read sequencing data 1
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
Shovill Faster SPAdes assembly of Illumina reads 7
Show-Coords Parse delta file and report coordinates and other information Read mapping Sequence alignment 5
showfeat Show features of a sequence 5
SHtest Use RAxML to calculate SHtest to compare trees 1
shuffleseq Shuffles a set of sequences maintaining composition 5
SICER Statistical approach for the Identification of ChIP-Enriched Regions 3
Sickle windowed adaptive trimming of FASTQ data 4
sigcleave Reports protein signal cleavage sites 5
SignalP 3.0 Find signal peptides in protein sequences 3
Similar Sequence Remover Removes characters in a sequence 1
SINA reference based multiple sequence alignment 5
sirna Finds siRNA duplexes in mRNA 5
sixpack Display a DNA sequence with 6-frame translation and ORFs 7
skipseq Reads and writes sequences, skipping first few 5
Slamdunk - streamlining SLAM-seq analysis with ultra-high sensitivity 6
Slice BAM by genomic regions 5
Slice VCF to get data from selected regions 1
SMAP compare (BETA) 1
SMAP delineate (BETA) 1
SMAP haplotype-sites (BETA) 1
sniffles Structural variation caller using third generation sequencing 1
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 11
snippy-clean_full_aln Replace any non-standard sequence characters in snippy 'core.full.aln' file. 4
snippy-core Combine multiple Snippy outputs into a core SNP alignment 11
SNP distance matrix Compute distance in SNPs between all sequences in a FASTA file 2
SnpEff build: database from Genbank or GFF record 12
SnpEff chromosome-info: list chromosome names/lengths 7
SnpEff databases: list available databases 12
SnpEff download: download a pre-built database 15
SnpEff eff: annotate variants 13
SnpEff eff: annotate variants for SARS-CoV-2 1
snpFreq significant SNPs in case-control data 2
SnpSift Annotate SNPs from dbSnp 8
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 8
SnpSift Extract Fields from a VCF file into a tabular file 6
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift GeneSets Annotating GeneSets, such as Gene Ontology, KEGG, Reactome 4
SnpSift Intervals Filter variants using intervals 8
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for VCF specification compliance 7
socru Calculate the order and orientation of complete bacterial genomes 1
Sort data in ascending or descending order 3
Sort data in ascending or descending order 10
Sort a row according to their columns 11
Sort assembly 4
Sort Column Order by heading 1
Sort.seqs put sequences in different files in the same order 6
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for regular and single-cell projects Genome assembly 13
Spaln: align cDNA or Protein to genome Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 4
Sparse Matrix Functions for manipulating 2-D Scipy sparse numeric data 11
Split BAM datasets on variety of attributes 3
Split BAM dataset on readgroups 4
Split BAM datasets on variety of attributes 2
Split a HUMAnN2 generated table 4
Split Dataset into training and test subsets 6
Split file to dataset collection 7
Split MAF blocks by Species 1
Split objects Split binary image by using watershed 1
Split stratified table 3
Split.abund Separate sequences into rare and abundant groups 5
Split.groups Generates a fasta file for each group 5
splitter Split a sequence into (overlapping) smaller sequences 5
SpyBOAT wavelet analyzes image stacks 1
SQLite to tabular for SQL query 3
Stacking Ensembles builds stacking, voting ensemble models with numerous base options 8
Stacks: assemble read pairs by locus run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers 6
Stacks: cstacks build a catalogue of loci 4
Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 5
Stacks: genotypes analyse haplotypes or genotypes in a genetic cross ('genotypes' program) 5
Stacks: populations analyze a population of individual samples ('populations' program) 5
Stacks: process radtags the Stacks demultiplexing script 5
Stacks: pstacks find stacks from short reads mapped to a reference genome 5
Stacks: reference map the Stacks pipeline with a reference genome (ref_map.pl) 5
Stacks: rxstacks make corrections to genotype and haplotype calls 5
Stacks: sstacks match stacks to a catalog 5
Stacks: ustacks align short reads into stacks 5
STAR-Fusion detect fusion genes in RNA-Seq data 4
staramr Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. 9
Starting Modules load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups) 2
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
Stop_supp To analyse Ribo-seq alignments for the detection of stop codon readthrough events 1
Strelka Germline small variant caller for germline variation in small cohorts 2
Strelka Somatic small variant caller for somatic variation in tumor/normal sample pairs 1
StringTie transcript assembly and quantification 14
StringTie merge transcripts 8
Structure using multi-locus genotype data to investigate population structure 1
Sub.sample Create a sub sample 5
Submit consensus sequence to ENA 1
Subset columns from a VCF dataset 1
Subtract the intervals of two datasets Filtering 5
Subtract Whole Dataset from another dataset 2
Summarize taxonomy 1
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 6
Summary.seqs Summarize the quality of sequences 5
Summary.shared Summary of calculator values for OTUs 5
Summary.single Summary of calculator values for OTUs 6
Summary.tax Assign sequences to taxonomy 5
supermatcher Match large sequences against one or more other sequences 5
Support vector machines (SVMs) for classification 12
syco Synonymous codon usage Gribskov statistic plot 5
T Test for Two Samples 2
tab2trees Create pdf of phylogeny graphics from table of tree names and newick trees 1
Table Compute computes operations on table data 3
Tabular to CSV 1
Tabular to FASTQ converter Conversion 5
Tabular-to-FASTA converts tabular file to FASTA format 2
tac reverse a file (reverse cat) 8
Tag pileup frequency 3
Tagdust TagDust - A program to eliminate artifactual reads from next-generation sequencing data sets. 1
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 2
Taylor-Butina Clustering of molecular fingerprints 5
TB Variant Filter M. tuberculosis H37Rv VCF filter 3
TB Variant Report - generate HTML report from SnpEff annotated M.tb VCF(s) 3
TB-Profiler Profile Infer strain types and drug resistance markers from sequences 13
tcode Fickett TESTCODE statistic to identify protein-coding DNA 5
TEtranscripts annotates reads to genes and transposable elements 3
TETyper Transposable Element Typer 3
Text reformatting with awk 12
Text transformation with sed 10
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
Thinning_trees Sub-sample trees from from a posterior distribution 1
tmap Displays membrane spanning regions 5
TMHMM 2.0 Find transmembrane domains in protein sequences 4
tnt2table Converts TNT text output from Morphobank into UCSB-phylotable. 1
TopHat Gapped-read mapper for RNA-seq data 9
Tophat Fusion Post post-processing to identify fusion genes 2
Train Augustus ab-initio gene predictor 5
Train SNAP ab-initio gene predictor 1
Train, Test and Evaluation fit a model using part of dataset and evaluate using the rest 7
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 5
TransDecoder finds coding regions within transcripts 7
transeq Translate nucleic acid sequences 5
Translate Runs Translate 1
Translate BED transcripts cDNA in 3frames or CDS 1
Transpose rows/columns in a tabular file 3
TransTermHP finds rho-independent transcription terminators in bacterial genomes 2
Tree.shared Generate a newick tree for dissimilarity among groups 5
tree_support Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees 1
TreeVector Draw a Phylogenic Tree 1
Trim leading or trailing characters 2
Trim Galore! Quality and adapter trimmer of reads 9
Trim sequences 5
Trim.flows partition by barcode, trim to length, cull by length and mismatches 5
Trim.seqs Trim sequences - primers, barcodes, quality 5
trimest Trim poly-A tails off EST sequences 5
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
trimseq Trim ambiguous bits off the ends of sequences 5
Trinity de novo assembly of RNA-Seq data 15
Trinotate 4
Triplet Periodicity (Step 2) Plot triplet periodicity for different read lengths. 1
twoBitToFa Convert all or part of .2bit file to FASTA 3
twofeat Finds neighbouring pairs of features in sequences 5
tximport Summarize transcript-level estimates for gene-level analysis 3
UCSB Hamster UCSB Hamster is a Galaxy port for the Hamster script which finds orthologs based on HMM's. 1
UMI-tools count performs quantification of UMIs from BAM files 9
UMI-tools deduplicate Extract UMI from fastq files 6
UMI-tools extract Extract UMI from fastq files 12
Unfold columns from a table 10
unifrac.unweighted Describes whether two or more communities have the same structure 5
unifrac.weighted Describes whether two or more communities have the same structure 5
union Reads sequence fragments and builds one sequence 5
Unipept retrieve taxonomy for peptides 5
UniProt ID mapping and retrieval 3
Unique occurrences of each record 8
Unique occurrences of each record 1
Unique lines assuming sorted input file 10
Unique.seqs Return unique sequences 5
Univariate Univariate statistics 2
Unpack pathway abundances to show genes included 3
Unzip Unzip file 1
Upload File from your computer Query and retrieval 3
UpSet diagram of intersection of genomic regions or list sets 2
VALET to detect mis-assemblies in metagenomic assemblies 1
ValidateSamFile assess validity of SAM/BAM dataset 14
VarDict calls SNVs and indels for tumor-normal pairs 4
Variant Annotator process variant counts 3
VarScan copynumber Determine relative tumor copy number from tumor-normal pileups 4
VarScan mpileup for variant detection 4
VarScan somatic Call germline/somatic and LOH variants from tumor-normal sample pairs 9
VCF to MAF Custom Track for display at UCSC 2
VCF to pgSnp Convert from VCF to pgSnp format 1
VCF-BEDintersect: Intersect VCF and BED datasets 5
VCF-VCFintersect: Intersect two VCF datasets 5
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 5
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 5
vcfanno VCF annotation 2
VCFannotate: Intersect VCF records with BED annotations 5
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 5
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 5
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 6
VCFcommonSamples: Output records belonging to samples common between two datasets 5
VCFdistance: Calculate distance to the nearest variant 5
VCFfilter: filter VCF data in a variety of attributes 8
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 5
VCFgenotypes: Convert numerical representation of genotypes to allelic 5
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 5
VCFleftAlign: Left-align indels and complex variants in VCF dataset 5
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 5
VCFselectsamples: Select samples from a VCF dataset 5
VCFsort: Sort VCF dataset by coordinate 6
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 6
vectorstrip Strips out DNA between a pair of vector sequences 5
Vegan Diversity index 3
Vegan Fisher Alpha index 3
Vegan Rarefaction curve and statistics 3
velvetg Velvet sequence assembler for very short reads De-novo assembly Formatting 6
velveth Prepare a dataset for the Velvet velvetg Assembler De-novo assembly Formatting 6
VelvetOptimiser Automatically optimize Velvet assemblies 5
Venn Generate Venn diagrams for groups 5
Venn diagram [JVenn] 4
vert_tree_format Convert between phylogenetic tree file formats 1
vg convert 1
vg deconstruct construct a dynamic succinct variation graph 1
vg view 1
Violin plot w ggplot2 5
Visualize the optimal scoring subnetwork 2
Visualize with Krona Visualise any hierarchical data 1
Volcano Plot create a volcano plot Visualisation 5
VSearch alignment Chimera detection Sequence clustering Sequence masking 6
VSearch chimera detection Chimera detection Sequence clustering Sequence masking 6
VSearch clustering Chimera detection Sequence clustering Sequence masking 7
VSearch dereplication Chimera detection Sequence clustering Sequence masking 7
VSearch masking Chimera detection Sequence clustering Sequence masking 6
VSearch search Chimera detection Sequence clustering Sequence masking 6
VSearch shuffling Chimera detection Sequence clustering Sequence masking 6
VSearch sorting Chimera detection Sequence clustering Sequence masking 7
VT normalize normalizes variants in a VCF file 1
water Smith-Waterman local alignment 5
Wavelet variance using Discrete Wavelet Transfoms 3
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
wobble Wobble base plot 5
WoLF PSORT Eukaryote protein subcellular localization prediction 3
wordcount Counts words of a specified size in a DNA sequence 5
wordmatch Finds all exact matches of a given size between 2 sequences 5
xcms adjustRtime (retcor) Retention Time Correction 7
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 8
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 5
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 8
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 5
XPath compute xpath expressions on XML data 2
XTandemAdapter Annotates MS/MS spectra using X! Tandem. 5
zerone 1