1736 tool(s) found

Tool Description Topics Available version(s)
[5.15-54.0] Interproscan functional predictions of ORFs Interproscan functional predictions of ORFs 2
aaChanges amino-acid changes caused by a set of SNPs 2
ABRicate 3
ABRicate List 3
Abundance Distribution Calculate abundance distribution of k-mers using pre-made k-mer countgraphs 2
Abundance Distribution (all-in-one) Calculate abundance distribution of k-mers 2
AccurateMassSearch Find potential HMDB ids within the given mass error window. 2
Add column to an existing dataset 3
Add hydrogen atoms at a certain pH value 1
Add input name as column to an existing tabular file 1
Add or Replace Groups 3
add-read-counts Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file 3
AddCommentsToBam add comments to BAM dataset 11
AdditiveSeries Computes an additive series to quantify a peptide in a set of samples. 4
AddOrReplaceReadGroups add or replaces read group information 11
Admixture : Map genomic intervals resembling specified source populations 1
Aggregate datapoints Appends the average, min, max of datapoints per interval 1
Aggregate Individuals : Append summary columns for a population 1
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 11
Align sequences using a variety of alignment methods (align_seqs) 3
Align.check Calculate the number of potentially misaligned bases 5
Align.seqs Align sequences to a template alignment 5
alignmentsieve Filter BAM/CRAM files according to specified parameters 5
alimask append modelmask line to a multiple sequence alignments 5
Amova Analysis of molecular variance 5
Analyze statistical significance of sample groupings using distance matrices (compare_categories) 3
Ancestry : Characterize ancestries w.r.t. inferred ancestral populations 1
Annotate a VCF dataset with custom filters 2
Annotate opens an IFrame to Apollo 1
Annotate DE(X)Seq result 1
Annotate tree 2
Annotate with DGI database info 1
Annotate with DGI database info 1
AnnotateBed annotate coverage of features from multiple files 17
annotateMyIDs annotate a generic set of identifiers 2
annotateMyIDs annotate a generic set of identifiers 1
Anosim Non-parametric multivariate analysis of changes in community structure 5
Anova N-way anova. With ou Without interactions 5
antaRNA Ant Colony Optimized RNA Sequence Design 1
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 4
Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 3
Apply Variant Recalibration 4
Arithmetic Operations on tables 2
Assemble with MIRA v3.4 Takes Sanger, Roche, Illumina, and Ion Torrent data 2
Assembly of long and error-prone reads 1
Assign taxonomy to each sequence (assign_taxonomy) 3
Associate HUMAnN2 functions with metadata 1
Augustus gene prediction for prokaryotic and eukaryotic genomes 4
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 5
BAM filter Removes reads from a BAM file based on criteria 5
BAM Index Statistics 3
BAM to BED converter 21
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 9
BAM-to-SAM convert BAM to SAM 8
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 9
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM file 16
BamHash Hash BAM and FASTQ files to verify data integrity 1
BamLeftAlign indels in BAM datasets 7
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
banana Bending and curvature plot in B-DNA 5
Bandage Image visualize de novo assembly graphs 1
Bandage Info determine statistics of de novo assembly graphs 1
Bar chart for multiple columns 1
Barcode Splitter 6
Barplot stratified HUMAnN2 features 1
Base Count 1
Base Coverage of all intervals Quantification 5
Base Recalibrator calculates covariates used to recalibrate base quality scores of reads 4
BaselineFilter Removes the baseline from profile spectra using a top-hat filter. 3
Batch_correction Corrects intensities for signal drift and batch-effects 8
bcftools call SNP/indel variant calling from VCF/BCF 7
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
bcftoolsView Convert, filter, subset VCF/BCF files 1
BEAM significant single- and multi-locus SNP associations in case-control studies 1
BED to BAM converter 18
BED to IGV create batch script for taking IGV screenshots 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BedCov calculate read depth for a set of genomic intervals 4
BEDPE to BAM converter 18
BedToIntervalList convert coordinate data into picard interval list format 11
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
bigwigCorrelate correlates pairs of BigWig files 2
bigWigToBedGraph Convert from bigWig to bedGraph format 3
Bin.seqs Order Sequences by OTU 5
Biom.info create shared and taxonomy files from biom 3
biosed Replace or delete sequence sections 5
Biosigner Molecular signature discovery from omics data 3
Bismark bisulfite mapper (bowtie) 1
Bismark bisulfite mapper (bowtie2) 3
Bismark Deduplicate Deduplicates reads mapped by Bismark 2
Bismark Meth. Extractor Reports on methylation status of reads mapped by Bismark 3
Bismark Pretty Report Generates a graphical HTML report page from report outputs of Bismark 2
BLAST parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input 2
BLAST Reciprocal Best Hits (RBH) from two FASTA files 4
BLAST top hit descriptions Make a table from BLAST XML 2
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Blast2GO Maps BLAST results to GO annotation terms 2
blockbuster detects blocks of overlapping reads using a gaussian-distribution approach 4
BlockClust efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles 1
Bowtie2 - map reads against reference genome 22
Boxplot of quality statistics 2
btwisted Calculates the twisting in a B-DNA sequence 5
Build a UPGMA tree comparing samples (upgma_cluster) 2
Build base quality distribution 2
Build custom track for UCSC genome browser 3
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 11
bwameth Fast and accurate aligner of BS-Seq reads. 3
bwtool-lift Project data base-by-base into a new assembly using a liftOver chain file from UCSC 1
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 1
Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) 3
Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables (beta_diversity) 3
Calculate metrics for classification performance 2
Calculate metrics for regression performance 1
Calculate protein properties 2
Call and phase heterozygous SNPs 4
Call SNPS with Freebayes Bayesian genetic variant detector 1
Calling of methylated regions 1
CalMD recalculate MD/NM tags 3
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 8
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 8
Canonical Correlation Analysis 2
Canu assembler Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore 1
cast expand combinations of variables:values to columnar format 2
Categorize by function collapse hierarchical data to a specified level 2
Categorize Elements satisfying criteria 2
CCAT Control-based ChIP-seq Analysis Tool 1
CD-HIT PROTEIN Cluster a protein dataset into representative sequences 4
CD-HIT-EST Cluster a nucleotide dataset into representative sequences 3
Change Case of selected columns 1
Change Title to meta-data value. 1
Change Title to meta-data value. 1
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 4
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 4
Check user's metadata mapping file for required data, valid format (validate_mapping_file) 2
checktrans Reports STOP codons and ORF statistics of a protein 4
Chimera.bellerophon Find putative chimeras using bellerophon 5
Chimera.ccode Find putative chimeras using ccode 5
Chimera.check Find putative chimeras using chimeraCheck 5
Chimera.perseus Find putative chimeras using chimeraCheck 5
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 3
chips Codon usage statistics 5
ChIPseeker for ChIP peak annotation and visualization 3
ChiRA Chimeric Read Annotator 1
Chop.seqs Trim sequences to a specified length 5
Chromatra L for visualizing genome-wide chromatin modifications 1
Chromatra T for visualizing genome-wide chromatin modifications 1
CIRCexplorer 2
Circos Builder creates circos plots from standard bioinformatics datatypes. 2
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 11
Clearcut Generate a tree using relaxed neighbor joining 5
Clip adapter sequences 5
CLIP Peakcaller find CLIP peaks in blockbuster data 1
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 9
Close relatives : Discover familial relationships 1
Closed-reference OTU picking Shotgun UniFrac workflow (pick_closed_reference_otus) 3
ClosestBed find the closest, potentially non-overlapping interval 17
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 5
Cluster KEGG : Group gene categories connected by shared genes 1
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 4
cluster_collection_report 3
ClusterBed cluster overlapping/nearby intervals 17
cmalign Align sequences to a covariance model against a sequence database 2
cmbuild Build covariance models from sequence alignments 3
cmfinder 2
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
cmpress Prepare a covariance model database for cmscan 1
cmscan Search sequences against collections of covariance models 1
cmsearch Search covariance model(s) against a sequence database 2
cmstat Summary statistics for covariance model 2
codcmp Codon usage table comparison 5
codeML Detects positive selection (paml package) 1
coderet Extract CDS, mRNA and translations from feature tables 5
Codon count gives numbers of all different codons in the whole sequence 1
Collapse sequences 4
Collapse Collection into single dataset in order of the collection 4
Collapse samples Collapse samples in a BIOM table and mapping file 1
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 11
Collect.shared Generate collector's curves for calculators on OTUs 5
Collect.single Generate collector's curves for OTUs 6
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 11
CollectGcBiasMetrics charts the GC bias metrics 11
CollectInsertSizeMetrics plots distribution of insert sizes 11
Collector’s curve of sequencing yield over time 1
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 12
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 11
Column arrange by header name 1
Column Join on Collections 3
Combine FASTA and QUAL into FASTQ 3
Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 1
Combine Variants 4
CometAdapter Annotates MS/MS spectra using Comet. 1
Compalignp Fractional identities between alignments 1
Compare multiple VCF datasets 2
Compare BIOM tables Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. 1
Compare outputs of HUMAnN2 for several samples and extract similar and specific information 1
Compare two Datasets to find common or distinct rows 1
Complement intervals of a dataset Sequence coordinate conversion 6
ComplementBed Extract intervals not represented by an interval file 18
CompNovo Performs a de novo peptide identification using the CompNovo engine. 3
CompNovoCID Performs a de novo peptide identification using the CompNovo engine. 3
Compound Convert Converts various chemistry and molecular modeling data files 1
Compound Convert Converts various chemistry and molecular modeling data files 1
Compound Search an advanced molecular grep program using SMARTS 1
compseq Count composition of dimer/trimer/etc words in a sequence 4
Compute an expression on every row 3
Compute beta diversity distance matrices and generate PCoA plots (beta_diversity_through_plots) 2
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
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 physico-chemical properties for a set of molecules 1
Compute quality statistics for SOLiD data 1
Compute quality statistics 4
Compute sequence length 5
computeGCBias Determine the GC bias of your sequenced reads 16
computeMatrix prepares data for plotting a heatmap or a profile of given regions 16
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 9
Concatenate FASTA alignment by species 2
Concatenate two datasets into one dataset Aggregation 6
Concatenate datasets tail-to-head 1
Concatenate datasets tail-to-head (cat) 5
Conformer calculation for molecules (confab) 2
Consensus.seqs Find a consensus sequence for each OTU or phylotype 5
ConsensusID Computes a consensus of peptide identifications of several identification engines. 4
ConsensusMapNormalizer Normalizes maps of one consensusXML file 3
Convert : CSV, FSTAT, Genepop or VCF to either gd_snp or gd_genotype 1
Convert sequences to graphs 1
Convert delimiters to TAB 1
Convert SOLiD output to fastq 1
Convert BAM to ScIdx 2
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to fai file 1
Convert FASTA to len file 1
Convert FASTA to Tabular 1
Convert from BAM to FastQ 14
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert GTF to BED12 1
Convert Kraken data to Galaxy taxonomy representation 3
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert OBO to OWL 1
Convert OBO to RDF 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to interval 2
Convert SAM to BAM without sorting 1
Convert tabular to dbnsfp 1
Convert uncompressed BCF to BCF 1
Convert, Merge, Randomize BAM datasets and perform other transformations 4
Cooccurrence tests whether presence-absence patterns differ from chance 5
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Correlation for numeric columns 2
Correlation matrix 1
Count occurrences of each record 2
Count Covariates on BAM files 2
Count GFF Features 3
Count Median Count the median/avg k-mer abundance for each sequence 2
Count sequences Count the sequences in a fasta file 1
Count the sequences in a fasta file (count_seqs) 2
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 5
Coverage Distributions : Examine sequence coverage for SNPs 1
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 4
Create a BedGraph of genome coverage 4
Create a genus level gene families file 1
Create a histogram of genome coverage 4
Create assemblies with Unicycler 7
Create binary barcodes from regular barcodes. 2
Create Decoy Database (reverse) Creates a decoy search database by adding reverse sequences to an existing database 1
Create nested list based on filenames and batch sizes 1
Create or Update Organism will create the organism if it doesn't exist, and update otherwise 1
Create single interval as a new dataset 1
Create text file with recurring lines 6
Create three-dimensional PCoA plots to be visualized with Emperor (make_emperor) 2
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 4
CRISPR Recognition Tool (CRT) 1
CTD analysis of chemicals, diseases, or genes 2
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 14
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 13
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
Cuffnorm Create normalized expression levels 5
Cuffquant Precompute gene expression levels 5
cummeRbund visualize Cuffdiff output 3
cusp Create a codon usage table 5
Cut columns from a table (cut) 6
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 13
cutseq Removes a specified section from a sequence 4
CVInspector A tool for visualization and validation of PSI mapping and CV files. 3
dan Calculates DNA RNA/DNA melting temperature 4
Data Fetch 1
DatabaseFilter Filters a protein database (FASTA format) based on identified proteins 2
Datamash (operations on tabular data) 3
DAVID functional annotation for a list of genes 1
Decharger Decharges and merges different feature charge variants of the same peptide. 3
DecoyDatabase Create decoy protein DB from forward protein DB. 2
Degap.seqs Remove gap characters from sequences 5
degapseq Removes gap characters from sequences 5
Delete an Apollo record 1
Delete Overlapping Indels from a chromosome indels file 2
Deletion Profile calculates the distributions of deleted nucleotides across reads 3
DeMeanderize Orders the spectra of MALDI spotting plates correctly. 2
Depth of Coverage on BAM files 4
Describe samples and replicates 9
Descriptors calculated with RDKit 1
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 15
detect CRISPR sequences (minced) 1
Determine_batch_correction to choose between linear, lowess and loess methods 5
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 5
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 5
DEXSeq-Map Maps the DEXSeq couting bins back to the transcript and exon ids 1
Diamond alignment tool for short sequences against a protein database 5
Diamond makedb Build database from a FASTA file 5
DiffBind differential binding analysis of ChIP-Seq peak data 12
Differential Cleavage : Select SNPs differentially cut by specified restriction enzymes 1
Differential expression analysis using a Trinity assembly 11
diffseq Find differences between nearly identical sequences 4
digest Protein proteolytic enzyme or reagent cleavage digest 5
Digestor Digests a protein database in-silico. 2
DigestorMotif digests a protein database in-silico 3
DISCO to assemble metagenomics data using an overlap-layout-consensus (OLC) approach 1
Discriminant Analysis 2
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
Diversity : pi, allowing for unsequenced intervals 1
Docking Tool to running molecular docking with Autodock Vina 1
DotKnot pseudoknot prediction in a given RNA sequence 1
dotmatcher Displays a thresholded dotplot of two sequences 4
dotpath Non-overlapping wordmatch dotplot of two sequences 4
dottup Displays a wordmatch dotplot of two sequences 4
Download and Extract Reads in BAM format from NCBI SRA 12
Download and Extract Reads in FASTA/Q format from NCBI SRA 12
Download and Generate Pileup Format from NCBI SRA 11
Download run data from EBI Metagenomics database 1
Downsample SAM/BAM Downsample a file to retain a subset of the reads 11
Draw nucleotides distribution chart 4
Draw phylogeny 1
Draw quality score boxplot 5
Draw quality score boxplot for SOLiD data 1
Draw ROC plot on "Perform LDA" output 3
Draw Stacked Bar Plots for different categories and different criteria 2
Draw variants : show positions of SNVs and unsequenced intervals 1
dreg Regular expression search of a nucleotide sequence 5
DREME - Discriminative Regular Expression Motif Elicitation 1
Drug-likeness quantitative estimation (QED) 1
DTAExtractor Extracts spectra of an MS run file to several files in DTA format. 4
EBI Search to obtain search results on resources and services hosted at the EBI 2
Edena (assembling) 2
Edena (overlapping) 2
edgeR Perform differential expression of count data 4
EGA Download streamer data from the European Genome-phenome Archive in a secure manner 2
eggNOG Mapper functional sequence annotation by orthology 4
EGSEA easy and efficient ensemble gene set testing 2
EICExtractor Extracts intensities from dedicates positions in a LC/MS map 3
einverted Finds DNA inverted repeats 4
Ensemble methods for classification and regression 2
epestfind Finds PEST motifs as potential proteolytic cleavage sites 4
EpiCSeg - Chromatin segmentation 1
equicktandem Finds tandem repeats 4
ERPairFinder Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. 2
est2genome Align EST and genomic DNA sequences 4
Estimate Library Complexity 3
estimate-energy Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place 3
EstimateLibraryComplexity assess sequence library complexity from read sequences 11
estimateReadFiltering estimates the number of reads that would be filtered given certain criteria 5
etandem Looks for tandem repeats in a nucleotide sequence 4
ETE GeneTree splitter from a genetree using the ETE Toolkit 1
ETE lineage generator from a list of species/taxids using the ETE Toolkit 1
ETE mod manipulates tree topology by rooting, pruning or sorting branches 1
ETE species tree generator from a list of species using the ETE Toolkit 1
ETE taxa DB generator generates the ETE sqlite DB from the NCBI taxdump.tar.gz 1
Eval Variants 4
Evaluate pairwise distances or compute affinity or kernel for sets of samples 2
Exonerate pairwise sequence comparison 3
ExpandBed replicate lines based on lists of values in columns 17
Export to a Local File 2
Export to GraPhlAn 1
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
ExternalCalibration Applies an external mass recalibration. 4
Extract alignment ends from SAM or BAM 2
Extract and cluster differentially expressed transcripts from a Trinity assembly 10
Extract barcodes according to pattern 2
Extract CuffDiff tabular files from a cummeRbund database 2
Extract FASTQ in tabular format from a set of FAST5 files 1
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 1
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract nanopore events from a set of sequencing reads 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
Extract partitions Separate sequences that are annotated with partitions into grouped files 2
Extract reads in FASTA or FASTQ format from nanopore files 1
Extract sequences from GenBank files (CDS, gene ...) 1
Extract time and channel information from a set of FAST5 files 1
extract-boxed-sequences Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility 3
extractfeat Extract features from a sequence 4
extractseq Extract regions from a sequence 5
FalseDiscoveryRate Estimates the false discovery rate on peptide and protein level using decoy searches. 3
faSplit Split a FASTA file 2
FASTA header converter to append species information 1
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 3
Fasta nucleotide color plot 2
Fasta nucleotide color plot 1
FASTA Width formatter 4
FASTA-to-Tabular converter 3
fasta_to_gspan 2
fastp - fast all-in-one preprocessing for FASTQ files 5
FASTQ de-interlacer on paired end reads 3
FASTQ Groomer convert between various FASTQ quality formats 4
FASTQ interlacer on paired end reads 4
FASTQ joiner on paired end reads 6
FASTQ Masker by quality score 3
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads 3
FASTQ Summary Statistics by column Sequence assembly validation 3
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
FASTQ to FASTA converter 4
FASTQ to Tabular converter 4
FASTQ Trimmer by column 4
fastq-join - Joins two paired-end reads on the overlapping ends 4
Fastq.info Convert fastq to fasta and quality 5
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FastqToSam convert Fastq data into unaligned BAM 14
FASTTREE adjust short reads Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 4
Feature coverage 1
Feature Selection module, including univariate filter selection methods and recursive feature elimination algorithm 1
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 16
FeatureFinderCentroided Detects two-dimensional features in LC-MS data. 3
FeatureFinderIdentification Detects features in MS1 data based on peptide identifications. 3
FeatureFinderIsotopeWavelet Detects two-dimensional features in LC-MS data. 3
FeatureFinderMetabo Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 3
FeatureFinderMRM Detects two-dimensional features in LC-MS data. 3
FeatureFinderMultiplex Determination of peak ratios in LC-MS data 4
FeatureFinderSuperHirn Finds mass spectrometric features in mass spectra. 2
FeatureLinkerLabeled Groups corresponding isotope-labeled features in a feature map. 3
FeatureLinkerUnlabeled Groups corresponding features from multiple maps. 3
FeatureLinkerUnlabeledKD Groups corresponding features from multiple maps. 2
FeatureLinkerUnlabeledQT Groups corresponding features from multiple maps. 3
FEELnc FlExible Extraction of LncRNA 2
Fetch closest non-overlapping feature for every interval Filtering 4
Fetch Indels from 3-way alignments 2
Fetch taxonomic representation 2
FFEval Evaluation tool for feature detection algorithms. 2
FidoAdapter Runs the protein inference engine Fido. 5
FileConverter Converts between different MS file formats. 4
FileFilter Extracts or manipulates portions of data from peak, feature or consensus-feature files. 4
FileInfo Shows basic information about the file, such as data ranges and file type. 3
FileMerger Merges several MS files into one file. 3
Filter a VCF file 2
Filter BAM datasets on a variety of attributes 6
Filter a set of molecules from a file 1
Filter data on any column using simple expressions Formatting 1
Filter BED on splice junctions that are not in a reference bed file 1
Filter by FASTA IDs Extract sequences from a FASTA file based on a list of IDs 2
Filter by quality 5
Filter Combined Transcripts using tracking file 1
Filter fasta to remove sequences based on input criteria (filter_fasta) 2
Filter FASTQ reads by quality score and length 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 1
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Filter OTUs from an OTU table based on their observation counts or identifier (filter_otus_from_otu_table) 2
Filter pileup on coverage and SNPs 3
Filter reads by minimal k-mer abundance 2
Filter reads below k-mer abundance of 50 2
Filter SAM on bitwise flag values 2
Filter SAM or BAM files on FLAG MAPQ RG LN or by region Filtering Nucleic acid sequence analysis 3
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
Filter sequence alignment by removing highly variable regions (filter_alignment) 3
Filter sequences by ID from a tabular file 5
Filter sequences by length Filtering 5
Filter sequences by mapping from SAM/BAM file 3
Filter SNPs : Discard some SNPs based on coverage, quality or spacing 1
Filter Tabular 4
Filter taxa from an OTU table (filter_taxa_from_otu_table) 2
Filter with SortMeRNA Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data 6
Filter with SortMeRNA Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data 1
filter-annotated-entries Split entries into two files based on whether they overlap annotations in a bed file 3
filter-by-energy Split entries over two files based on the estimated energy 3
Filter.seqs removes columns from alignments 5
Filter.shared remove OTUs based on various critieria 5
Filtering of methylated regions 1
Filters samples from an OTU table on the basis of the number of observations in that sample, or on the basis of sample metadata (filter_samples_from_otu_table) 2
FilterSamReads include or exclude aligned and unaligned reads and read lists 11
filtlong Filtering long reads by quality 1
FIMO - Find Individual Motif Occurrences 9
Find diagnostic hits 1
Find differentially methylated region (DMR) 1
find in reference filter peptides that are present in proteins 3
Find lowest diagnostic rank 1
find-boxes Finds all occurances of two given boxes (sequence motifs) within a FASTA file 3
FisherBed calculate Fisher statistic between two feature files 17
Fit a BUM model with p-values 1
fix-fasta-headers Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file 3
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 11
Flagstat tabulate descriptive stats for BAM datset 8
FlankBed create new intervals from the flanks of existing intervals 18
Flanking Sequence : Fetch DNA sequence for intervals surrounding the given SNPs 1
FLASH adjust length of short reads 4
FlashLFQ ultrafast label-free quantification for mass-spectrometry proteomics 1
fold change heatmap Plot heat map of fold changes from multiple DESeq2 outputs 1
Format tree and trait tables 1
Format cd-hit outputs to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 1
Format Fastq sequences and barcode data (extract_barcodes) 2
Format MetaPhlAn2 output to extract abundance at different taxonomic levels 1
Format MetaPhlAn2 output for Krona 1
Founders sequenced : Offspring estimated heterozygosity from a pedigree with sequenced founders 1
FPKM Count calculates raw read count, FPM, and FPKM for each gene 5
FragGeneScan for finding (fragmented) genes in short reads 1
Fragmenter splits a molecule in fragments 1
freak Residue/base frequency table or plot 4
FreeBayes bayesian genetic variant detector 7
FunDO human genes associated with disease terms 3
fuzznuc Nucleic acid pattern search 5
fuzzpro Protein pattern search 4
fuzztran Protein pattern search after translation 4
FuzzyDiff Compares two files, tolerating numeric differences. 2
g:Profiler tools for functional profiling of gene lists 1
garnier Predicts protein secondary structure 5
gd_snp to VCF : Convert from gd_snp or gd_genotype to VCF format, for submission to dbSNP 1
geecee Calculates fractional GC content of nucleic acid sequences 5
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 1
GEMINI amend Amend an already loaded GEMINI database. 1
GEMINI annotate adding your own custom annotations 4
GEMINI autosomal recessive/dominant Find variants meeting an autosomal recessive/dominant model 4
GEMINI burden perform sample-wise gene-level burden calculations 3
GEMINI comp_hets Identifying potential compound heterozygotes 3
GEMINI db_info List the gemini database tables and columns 3
GEMINI de_novo Identifying potential de novo mutations 3
GEMINI dump Extract data from the Gemini DB 1
GEMINI fusions Identify somatic fusion genes from a GEMINI database 2
GEMINI gene_wise Custom genotype filtering by gene 1
GEMINI interactions Find genes among variants that are interacting partners 3
GEMINI load Loading a VCF file into GEMINI 3
GEMINI lof_sieve Filter LoF variants by transcript position and type 3
GEMINI mendel_errors Identify candidate violations of Mendelian inheritance 1
GEMINI pathways Map genes and variants to KEGG pathways 3
GEMINI qc Quality control tool 1
GEMINI query Querying the GEMINI database 4
GEMINI region Extracting variants from specific regions or genes 3
GEMINI roh Identifying runs of homozygosity 3
GEMINI set_somatic Tag somatic mutations in a GEMINI database 1
GEMINI stats Compute useful variant statistics 3
GEMINI windower Conducting analyses on genome "windows" 3
GenBank and EBML to GFF converter 1
Genbank to GFF3 converter 2
Gene Align and Family Aggregator generates an SQLite database that can be visualised with Aequatus 2
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 11
Gene Body Coverage (Bigwig) Read coverage over gene body 11
Gene length and GC content from GTF and FASTA file 2
Generalized linear models for classification and regression 2
Generate random samples with controlled size and complexity 2
Generate A Matrix for using PC and LDA 2
Generate box-whisker plot of quality score distribution over positions in nanopore reads 1
Generate gene to transcript map for Trinity assembly 11
Generate heatmap with hierarchical clustering of both samplesand microbial clades for MetaPhlAn2 1
Generate histogram of nanopore read lengths 1
Generate pileup from BAM dataset 3
Generate SuperTranscripts from a Trinity assembly 5
Generic_Filter Removes elements according to numerical or qualitative values 4
GeneSeqToFamily preparation converts data for the workflow 2
Genome annotation statistics 1
Genome Coverage compute the coverage over an entire genome 18
Get all term synonyms of a given OBO term 1
Get all terms of a given OBO term 1
Get all the relationship IDs and definitions from the given OBO ontology 1
Get all the relationship IDs and names from the given OBO ontology 1
Get all the relationship IDs and namespaces from the given OBO ontology 1
Get all the relationship types from the given OBO ontology 1
Get all the term IDs and term names of a given OBO ontology 1
Get child terms of a given OBO term 1
Get crosslinked nucleotides from full alignments 2
Get features by Ensembl ID using REST API 2
Get flanks returns flanking region/s for every gene Sequence analysis 5
Get gene tree by Ensembl ID using REST API 2
Get longest read from a set of FAST5 files. 1
Get Microbial Data 1
Get Pathways : Look up KEGG pathways for given Ensembl transcripts 1
Get RT Stop Counts derives the reverse transcriptase (RT) stop count on each nucleotide from a mapped file provided by the Iterative Mapping module 1
Get sequences by Ensembl ID using REST API 2
Get subontology from a given OBO term 1
Get the ancestor terms of a given OBO term Collects the ancestor terms from a given term in the given OBO ontology 2
Get the descendent terms of a given OBO term 1
Get the parent terms of a given OBO term 1
Get the root terms of a given OBO term 1
Get the terms filtered by a relationship type 1
Get the terms that are related by a concrete relationship type 1
Get.communitytype description 5
Get.coremicrobiome fraction of OTUs for samples or abundances 5
Get.dists selects distances from a phylip or column file 5
Get.group group names from shared or from list and group 5
Get.groups Select groups 5
Get.label label names from list, sabund, or rabund file 5
Get.lineage Picks by taxon 5
Get.mimarkspackage creates a mimarks package form with your groups 5
Get.otulabels Selects OTU labels 5
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 5
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 17
getorf Finds and extracts open reading frames (ORFs) 4
GFF converter to GenBank or embl 1
GFF-to-BED converter Conversion 1
GFF3 to Apollo Annotations 1
GffCompare compare assembled transcripts to a reference annotation 2
gffread Filters and/or converts GFF3/GTF2 records 3
Glimmer ICM builder 2
Glimmer3 Predict ORFs in prokaryotic genomes (not knowlegde-based) 2
Glimmer3 Predict ORFs in prokaryotic genomes (knowlegde-based) 2
GMAJ Multiple Alignment Viewer 1
Golm Metabolome Database search spectrum : GC-MS Mass Spectral Database. 2
goseq tests for overrepresented gene categories 4
GotohScan Find subsequences in db 1
GPASS significant single-SNP associations in case-control studies 1
GraphProt predict profile - Predict RBP binding profiles 1
GROMACS energy minimization of the system prior to equilibration and production MD 1
GROMACS initial setup of topology and GRO structure file 1
GROMACS NPT equilibration - constant-temperature and -pressure equilibration of a system 1
GROMACS NVT equilibration - constant-temperature and -volume equilibration of a system 1
GROMACS production simulation for data collection 1
GROMACS solvation and adding ions to structure and topology files 1
Group data by a column and perform aggregate operation on other columns. 3
Group abundances of UniRef50 gene families obtained (HUMAnN2 output) to Gene Ontology (GO) slim terms 1
GroupByBed group by common cols and summarize other cols 17
GTF-to-BEDGraph converter Conversion 1
Gubbins Recombination detection in Bacteria 1
Hammock - cluster peptides Clusters short peptide sequences 5
Haplotype Caller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region 3
Hardklor identification of features from mass spectra 2
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
hcluster_sg Hierarchically clustering on a sparse graph 2
hcluster_sg parser converts hcluster_sg 3-column output into lists of IDs 2
Heatmap Heatmap of the dataMatrix 3
Heatmap w ggplot 1
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 4
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 3
hicAggregateContacts allow plotting of aggregated Hi-C contacts between regions specified in a file 4
hicBuildMatrix creates a matrix of interactions 11
hicCompareMatrices normalize and compare two Hi-C contact matrices 4
hicCorrectMatrix Runs Dekker's iterative correction over a hic matrix. 10
hicCorrelate compute pairwise correlations between multiple Hi-C contact matrices 9
hicFindTADs find minimum cuts that correspond to boundaries 9
hicMergeMatrixBins Merges bins from a Hi-C matrix 8
hicPCA compute the principal components for A / B compartment analysis 6
hicPlotDistVsCounts compute distance vs Hi-C counts plot per chromosome 9
hicPlotMatrix Plots a HiC matrix heatmap 9
hicPlotTADs Plots the diagonal, and some values close to the diagonal of a HiC matrix 9
hicPlotViewpoint plot interactions around a viewpoint 5
hicSumMatrices combine Hi-C matrices of the same size 10
hicTransform transforms a matrix to a obs_exp, pearson and covariance matrix 5
Hicup Deduplicator removes duplicated di-tags (retaining one copy of each) from the data set. 3
Hicup Digester cuts throughout a selected genome at one or two specified restriction sites. 3
Hicup Filter classifies read pairs, identifying valid Hi-C di-tags. 3
Hicup Mapper aligns paired reads independently to a reference genome and retains reads where both partners align. 2
Hicup Pipeline controls the other programs in the HiCUP pipeline. 3
Hicup Truncater terminates sequence reads at specified Hi-C ligation junctions. 3
hifive manipulate, analyze, and plot HiC and 5C chromatin interaction data 2
HighResPrecursorMassCorrector Corrects the precursor mass and charge determined by the instrument software. 3
HISAT2 A fast and sensitive alignment program 16
Histogram of a numeric column 4
Histogram w ggplot2 2
HMDB MS search search by masses on HMDB online LCMS bank 3
hmmalign align sequences to a profile HMM 5
hmmbuild Build a profile HMM from an input multiple alignment 5
hmmconvert convert profile file to a HMMER format 5
hmmemit sample sequence(s) from a profile HMM 5
hmmfetch retrieve profile HMM(s) from a file 5
hmmscan search sequence(s) against a profile database 5
hmmsearch search profile(s) against a sequence database 5
hmoment Hydrophobic moment calculation 4
Homology Classifier and Filter from a genetree utilising the ETE Toolkit 1
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 2
HVIS visualization of genomic data with the Hilbert curve 3
Hyperparameter Search using exhausitive or randomized search 1
IDBA-UD Iterative de Bruijn Graph Assembler 1
IDConflictResolver Resolves ambiguous annotations of features with peptide identifications 4
idconvert Convert mass spectrometry identification files 2
IDDecoyProbability Estimates peptide probabilities using a decoy search strategy.WARNING: This util is deprecated. 3
Identify optimal scoring subnetwork using Heinz 1
IDExtractor Extracts 'n' peptides randomly or best 'n' from idXML files. 2
IDFileConverter Converts identification engine file formats. 4
IDFilter Filters results from protein or peptide identification engines based on different criteria. 3
IDMapper Assigns protein/peptide identifications to features or consensus features. 3
IDMassAccuracy Calculates a distribution of the mass error from given mass spectra and IDs. 3
IDMerger Merges several protein/peptide identification files into one file. 3
idpAssemble Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels. 2
idpEmbedder Embed human/mouse gene metadata into IDPicker files 2
IDPosteriorErrorProbability Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 3
idpQonvert Prepare identification results for IDPicker 2
idpQuery Creates text reports from idpDB files. 2
IDR compare ranked list of identifications 1
IDRipper Split protein/peptide identification file into several files according to annotated file origin. 3
IDRTCalibration Can be used to calibrate RTs of peptide hits linearly to standards. 3
IDScoreSwitcher Switches between different scores of peptide or protein hits in identification data 3
IDSplitter Splits protein/peptide identifications off of annotated data files 2
IdxStats tabulate mapping statistics for BAM dataset 9
iep Calculates the isoelectric point of a protein 4
Inbreeding and kinship : Analyze the pedigree without genomic data 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
InclusionExclusionListCreator Creates inclusion and/or exclusion lists. 3
Indel Realigner - perform local realignment 4
Indicator Identify indicator "species" for nodes on a tree 5
Infer Experiment speculates how RNA-seq were configured 11
infoseq Displays some simple information about sequences 5
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 11
Insertion Profile calculates the distribution of inserted nucleotides across reads 3
Insertion size metrics for PAIRED data 3
InspectAdapter Annotates MS/MS spectra using Inspect. 4
IntaRNA Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. 2
InternalCalibration Applies an internal mass recalibration. 4
InterProphet Combine Peptide Prophet results from multiple search engines 1
Intersect the intervals of two datasets Filtering 7
Intersect multiple VCF datasets 3
Intersect intervals find overlapping intervals in various ways 17
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 2
IsobaricAnalyzer Calculates isobaric quantitative values for peptides 3
isochore Plots isochores in large DNA sequences 4
Iterative Mapping iteratively maps the raw reads of RNA structural data to the reference transcriptome 1
IUPAC name-to-structure converter (OPSIN) 1
IWTomics Load Smooth and Plot 1
IWTomics Plot with Threshold on Test Scale 1
IWTomics Test and Plot 1
JaccardBed calculate the distribution of relative distances between two files 17
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 5
JAMM Calls peaks on NGS data 1
JBrowse genome browser 11
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance 7
Je-Clip clips Unique Molecular Identifiers (UMIs) from fastq files 2
Je-Demultiplex demultiplexes fastq files 2
Je-Demultiplex-Illu demultiplexes fastq files using Illumina Index file 2
Je-MarkDuplicates to filter BAM files for read duplicates taking UMIs into account 2
Join the intervals of two datasets side-by-side Aggregation 5
Join two files 7
Join HUMAnN2 generated tables 2
Join +/- Ions Join positive and negative ionization-mode W4M datasets for the same samples 1
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 3
Join two files on column allowing a small difference 1
JQ process JSON 1
Junction Annotation compares detected splice junctions to reference gene model 11
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 11
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 2
Kallisto quant - quantify abundances of RNA-Seq transcripts 4
Karyotype Plotting tool for multiple series 1
Kernel Canonical Correlation Analysis 3
Kernel Principal Component Analysis 3
Kinfold Simulates the stochastic folding kinetics of RNA sequences into secondary structures. 1
Kinwalker cotranscriptional folding of RNAs 1
KOBAS Annotate KEGG Orthology Based Annotation System 2
KOBAS Identify KEGG Orthology Based Annotation System 2
Kraken assign taxonomic labels to sequencing reads 6
Kraken taxonomic report view report of classification for multiple samples 2
Kraken-filter filter classification by confidence score 3
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 4
Kraken-translate convert taxonomy IDs to names 3
Krona pie chart from taxonomic profile 8
Kronik processes Hardklor features to find peptides by chromatographic profiling 2
Label free protein summarisation and quantitation 1
LabeledEval Evaluation tool for isotope-labeled quantitation experiments. 2
LAJ Pairwise Alignment Viewer 1
LASTZ : align long sequences 5
Lastz paired reads map short paired reads against reference sequence 2
LASTZ_D : estimate substitution scores matrix 3
LAV to BED Converts a LAV formatted file to BED format 1
LCMS matching Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. 8
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
Libshuff Cramer-von Mises tests communities for the same structure 5
lighter can correct the reads containing sequence errors 1
limma Perform differential expression with limma-voom or limma-trend 10
lindna Draws linear maps of DNA constructs 4
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
List Organisms in Apollo 1
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
LocARNA Multiple Alignment and Folding of RNAs 1
locarna_graphclust 2
LowMemPeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 3
LowMemPeakPickerHiResRandomAccess Finds mass spectrometric peaks in profile mass spectra. 2
LPS LASSO-Patternsearch algorithm 1
LuciphorAdapter Modification site localisation using LuciPHOr2. 3
MACS Model-based Analysis of ChIP-Seq 4
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 9
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 11
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 8
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 8
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 8
MAF Coverage Stats Alignment coverage information 1
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
MAFFT Multiple alignment program for amino acid or nucleotide sequences 4
MAGeCK count - collect sgRNA read counts from read mapping files 5
MAGeCK GSEA - a fast implementation of Gene Set Enrichment Analysis 1
MAGeCK mle - perform maximum-likelihood estimation of gene essentiality scores 2
MAGeCK pathway - given a ranked gene list, test whether one pathway is enriched 1
MAGeCKs test - given a table of read counts, perform the sgRNA and gene ranking 2
Make Design Assign groups to Sets 5
Make File : Build a gd_snp or gd_genotype file 1
Make OTU table Make an OTU table from an OTU map and a taxonomy assignment file 1
Make phylogeny (make_phylogeny) 2
Make strain profiles 1
Make taxonomy summary charts based on taxonomy assignment (plot_taxa_summary) 2
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 5
Make.fastq Convert fasta and quality to fastq 5
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 5
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 6
Make.sra creates the necessary files for a NCBI submission 5
MakeWindowsBed make interval windows across a genome 18
MALDIquant peak detection Peak detection, binning and filtering for mass-spectrometry imaging data 1
MALDIquant preprocessing Preprocessing of mass-spectrometry imaging data 1
Manipulate FASTQ reads on various attributes 3
Mantel Mantel correlation coefficient between two matrices. 5
Map peptides to a bed file for viewing in a genome browser 2
Map with BFAST 1
Map with Bowtie for Illumina 8
Map with Bowtie for SOLiD 1
Map with BWA - map short reads (< 100 bp) against reference genome 15
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 17
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences 6
Map with Mosaik 1
Map with PerM for SOLiD and Illumina 1
MapAlignerIdentification Corrects retention time distortions between maps based on common peptide identifications. 2
MapAlignerPoseClustering Corrects retention time distortions between maps using a pose clustering approach. 3
MapAlignerSpectrum Corrects retention time distortions between maps by spectrum alignment. 2
MapBed apply a function to a column for each overlapping interval 17
MapNormalizer Normalizes peak intensities in an MS run. 3
Mapper for long, error-prone reads, like Nanopore ONT and PacBio 1
MapRTTransformer Applies retention time transformations to maps. 4
MapStatistics Extract extended statistics on the features of a map for quality control. 3
Mark Duplicate reads 3
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 11
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 11
marscan Finds MAR/SAR sites in nucleic sequences 5
MascotAdapter Annotates MS/MS spectra using Mascot. 3
MascotAdapterOnline Annotates MS/MS spectra using Mascot. 3
maSigPro Significant Gene Expression Profile Differences in Time Course Gene Expression Data 3
MaskFastaBed use intervals to mask sequences from a FASTA file 17
maskfeat Mask off features of a sequence 5
maskseq Mask off regions of a sequence 5
MassBank spectrum searches : Search by pseudo-spectra on a High Quality Mass Spectral Database. 1
MassCalculator Calculates masses and mass-to-charge ratios of peptide sequences 3
MassTraceExtractor Detects mass traces in centroided LC-MS data. 2
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
matcher Finds the best local alignments between two sequences 4
Matings : Assignment of optimal breeding pairs 1
MDS Scatter Plot of molecule similarity 1
MeanQualityByCycle chart distribution of base qualities 11
Megablast compare short reads against htgs, nt, and wgs databases 3
MEGAHIT metagenomics assembly 4
megamerger Merge two large overlapping nucleic acid sequences 4
melt collapse combinations of variables:values to single lines 2
MEME - Multiple Em for Motif Elicitation 10
MEME psp-gen - perform discriminative motif discovery 3
MEME-ChIP - motif discovery, enrichment analysis and clustering on large nucleotide datasets 1
Merge multiple VCF datasets 3
Merge MetaPhlAn2 files 1
Merge the overlapping intervals of a dataset Sequence merging 5
Merge BAM Files merges BAM files together 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge BedGraph files 4
Merge Columns together 2
Merge paired reads Merges two fastq paired-reads files into one file. 1
Merge PCR duplicates according to UMIs 2
Merge.count Merge count tables 3
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 5
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 11
MergeBED combine overlapping/nearby intervals into a single interval 17
merger Merge two overlapping nucleic acid sequences 4
MergeSamFiles merges multiple SAM/BAM datasets into one 11
Merging fragmented molecules 1
Merging sites from both strands (destrand) 1
MetaboliteAdductDecharger Decharges and merges different feature charge variants of the same metabolite. 1
MetaboliteSpectralMatcher Perform a spectral library search. 2
Metagenome Contributions of OTUs to user-specified functions 1
metagenomeSeq Normalization Cumulative sum scaling 1
metaMS.runGC GC-MS data preprocessing using metaMS package 4
MetaPhlAn2 metagenomic profiler V2 2
MetaProSIP Performs proteinSIP on peptide features for elemental flux analysis. 2
metaSPAdes assembler for metagenomics datasets 3
Metastats generate principle components plot data 5
metilene calling differentially methylated regions from bisulfite sequencing data 4
MiGMAP mapper for full-length T- and B-cell repertoire sequencing 2
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. 2
MiModD NacreousMap maps phenotypically selected variants by multi-variant linkage analysis 2
MiModD Rebase Sites from a VCF file 2
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 2
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 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 2
MINE - Maximal Information-based Nonparametric Exploration 2
miRanda finds potential target sites for miRNAs in genomic sequences 2
MiRDeep2 identification of novel and known miRNAs 3
MiRDeep2 Mapper process and map reads to a reference genome 4
MiRDeep2 Quantifier fast quantitation of reads mapping to known miRBase precursors 2
Mismatch Profile calculates the distribution of mismatches across reads 3
Model Validation evaluates estimator performance by cross-validation 1
moFF extracts MS1 intensities from spectrum files 3
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
Molecule recognition in Images or PDF documents (OSRA) 2
Molecules to Fingerprints with different fingerprint types 2
Morpheus database search algorithm for high-resolution tandem mass spectra 1
Motif_Finder_Plot 2
MPileup call variants 10
MRMMapper MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) 3
MRMPairFinder Util which can be used to evaluate labeled pair ratios on MRM features. 3
MRMTransitionGroupPicker Picks peaks in SRM/MRM chromatograms. 3
MS-GF+ Identifies peptides in tandem mass spectra using the MS-GF+ search engine. 5
MSABOOT Output PHYLIP file with bootstrapped multiple sequence alignment data 3
msbar Mutate sequence beyond all recognition 4
msconvert Convert and/or filter mass spectrometry files 2
msconvert (vendor support) Convert and/or filter mass spectrometry files (with vendor support on Windows) 1
MSGFPlusAdapter MS/MS database search using MS-GF+. 4
MSI classification spatial classification of mass spectrometry imaging data 1
MSI combine combine several mass spectrometry imaging datasets into one 6
MSI filtering tool for filtering mass spectrometry imaging data 8
MSI filtering tool for filtering mass spectrometry imaging data 1
MSI ion images mass spectrometry imaging m/z heatmaps 9
MSI massspectra mass spectrometry imaging mass spectra plots 8
MSI preprocessing mass spectrometry imaging preprocessing 8
MSI Qualitycontrol mass spectrometry imaging QC 8
MSI segmentation mass spectrometry imaging spatial clustering 6
MSSimulator A highly configurable simulator for mass spectrometry experiments. 2
Multi Compound Search an advanced molecular grep program using SMARTS 1
Multi-Join (combine multiple files) 6
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 17
multiBigwigSummary calculates average scores for a list of two or more bigwig files 17
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
Multiple Intersect identifies common intervals among multiple interval files 21
MultiplexResolver Completes peptide multiplets and resolves conflicts within them. 2
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 9
Multivariate PCA, PLS and OPLS 7
MUMmer dotplot Combine mummer/nucmer/promer with mummerplot 4
MUSCLE multiple aligner Multiple sequence alignment 2
Mutate Codons with SNPs 1
MyriMatch Identify peptides in tandem mass spectra. 2
MzMLSplitter Splits an mzML file into multiple parts 2
MzTabExporter Exports various XML formats to an mzTab file. 3
Naive Variant Caller - tabulate variable sites from BAM datasets 4
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 1
Nanopolish eventalign - Align nanopore events to reference k-mers 2
Nanopolish methylation - Classify nucleotides as methylated or not. 2
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 2
Natural Product likeness calculator 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 12
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 10
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 12
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI ECitMatch search NCBI for citations in PubMed 1
NCBI EFetch fetch records from NCBI 1
NCBI EGQuery Provides the number of records retrieved in all Entrez databases by a single text query. 1
NCBI EInfo fetch NCBI database metadata 1
NCBI ELink link UIDs from one database to another 1
NCBI EPost post UIDs to NCBI History Server 1
NCBI ESearch search NCBI Databases by text query 1
NCBI ESummary fetch summary of history/ids 1
Nearest Neighbors Classification 2
Nearest Neighbors Classification 1
needle Needleman-Wunsch global alignment 4
newcpgreport Report CpG rich areas 4
newcpgseek Reports CpG rich region 4
newseq Type in a short new sequence 5
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 5
nhmmscan search DNA sequence(s) against a DNA profile database 5
Nmds generate non-metric multidimensional scaling data 5
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 3
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 5
NMR_Normalization Normalization of NMR bucketed and integrated spectra 1
NMR_Preprocessing Preprocessing of 1D NMR spectra 3
NMR_Read Read Bruker NMR raw files 2
NoiseFilterGaussian Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). 3
NoiseFilterSGolay Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. 4
Nonpareil to estimate average coverage and generate Nonpareil curves 1
noreturn Removes carriage return from ASCII files 5
Normalization Normalization of (preprocessed) spectra 4
Normalize combined meta'omic sequencing data 1
Normalize By Median Filter reads using digital normalization via k-mer abundances Sequence file editing Sequence word comparison 4
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 11
notseq Exclude a set of sequences and write out the remaining ones 5
NSPDK_candidateClusters 2
NSPDK_sparseVect 2
nthseq Writes one sequence from a multiple set of sequences 4
NucBed profile the nucleotide content of intervals in a FASTA file 17
Nucleosome Predictions 1
Nucleotide Diversity : &pi; and &theta; 1
Nucleotide subsequence search providing regions in BED format 2
Numeric Clustering 2
Numeric Clustering 1
NxN Clustering of molecular fingerprints 2
ococo consensus caller on SAM/BAM 1
octanol Displays protein hydropathy 4
oddcomp Find protein sequence regions with a biased composition 4
Online data fetching ... 1
Open Molecule Generator Exhaustive generation of chemical structures 1
OpenPepXL Tool for protein-protein cross-linking identification using labeled linkers. 1
OpenPepXLLF Tool for protein-protein cross linking with label-free linkers. 1
OpenSwathAnalyzer Picks peaks and finds features in an SRM experiment. 3
OpenSwathAssayGenerator Generates assays according to different models for a specific TraML 3
OpenSwathChromatogramExtractor Extract chromatograms (XIC) from a MS2 map file. 2
OpenSwathConfidenceScoring Compute confidence scores for OpenSwath results 4
OpenSwathDecoyGenerator Generates decoys according to different models for a specific TraML 4
OpenSwathDIAPreScoring Scoring spectra using the DIA scores. 2
OpenSwathFeatureXMLToTSV Converts a featureXML to a mProphet tsv. 3
OpenSwathFileSplitter Splits SWATH files into n files, each containing one window. 3
OpenSwathMzMLFileCacher This tool caches the spectra and chromatogram data of an mzML to disk. 2
OpenSwathRewriteToFeatureXML Combines featureXML and mProphet tsv to FDR filtered featureXML. 3
OpenSwathRTNormalizer This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. 4
OpenSwathWorkflow Complete workflow to run OpenSWATH 2
OPLS-DA_Contrasts OPLS-DA Contrasts of Univariate Results 2
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
Overall FST : Estimate the relative fixation index between two populations 1
OverlapBed computes the amount of overlap from two intervals 17
Owler fast, trimmed overlap pipeline without aligning 1
Paired Read Mate Fixer for paired data 3
Pairs sequenced : Offspring estimated heterozygosity of sequenced pairs 1
Pairwise intersection and heatmap for genomic intervals 1
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
palindrome Looks for inverted repeats in a nucleotide sequence 4
Parallel Coordinates Plot of tabular data 1
PARalyzer A method to map interaction sites between RNA-binding proteins and their targets 1
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 10
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
pasteseq Insert one sequence into another 4
Pathway Image : Draw a KEGG pathway, highlighting specified gene modules 1
Pathway Matcher PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. 2
patmatdb Search a protein sequence with a motif 5
PCA : Principal Components Analysis of genotype data 2
Pca Principal Coordinate Analysis for a shared file 5
PCA plot w ggplot2 1
Pcoa Principal Coordinate Analysis for a distance matrix 4
Pcr.seqs Trim sequences 5
PEAKachu Calls Peaks in CLIP data 2
PeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 4
PeakPickerIterative Finds mass spectrometric peaks in profile mass spectra. 2
PeakPickerWavelet Finds mass spectrometric peaks in profile mass spectra. 4
Pear Paired-End read merger 4
pepcoil Predicts coiled coil regions 4
pepinfo Plots simple amino acid properties in parallel 4
pepnet Displays proteins as a helical net 5
pepstats Protein statistics 5
Peptide Prophet Calculate Peptide Prophet statistics on search results 1
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 10
PeptideIndexer Refreshes the protein references for all peptide hits. 3
pepwheel Shows protein sequences as helices 4
pepwindow Displays protein hydropathy 4
pepwindowall Displays protein hydropathy of a set of sequences 4
Per-SNP FSTs : Compute a fixation index score for each SNP 1
Percolator accurate peptide identification 1
PercolatorAdapter Facilitate input to Percolator and reintegrate. 1
Perform alpha rarefaction (alpha_rarefaction) 3
Perform Best-subsets Regression 2
Perform closed-reference OTU picking 1
Perform jackknifed UPGMA clustering and building jackknifed PCoA plots (jackknifed_beta_diversity) 2
Perform LDA Linear Discriminant Analysis 3
Perform open-reference OTU picking 1
Perform open-reference OTU picking (pick_open_reference_otus) 3
Perform OTU picking (pick_otus) 2
Perform taxonomy summaries and plots (summarize_taxa_through_plots) 2
pgma_graphclust 2
Pharmacophore generation (Align-it) 1
Pharmacophore Alignment and Optimization (Align-it) 1
phmmer search a protein sequence against a protein database (BLASTP-like) 5
PhosphoScoring Scores potential phosphorylation sites in order to localize the most probable sites. 3
Phylip : prepare data for phylogenetic analysis 1
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phylogenetic Tree : Show genetic relationships among individuals 1
phyloP interspecies conservation scores 1
Phylotype Assign sequences to OTUs based on taxonomy 5
Pick Primers : Find suitable PCR primers for SNPs 1
Pick representative set of sequences (pick_rep_set) 2
PileOMeth A tool for processing bisulfite sequencing alignments 5
Pileup-to-Interval condenses pileup format into ranges of bases 5
pilon An automated genome assembly improvement and variant detection tool 2
Pipeline Builder constructs a list of transforms and a final estimator 1
Piranha peak-caller for CLIP- and RIP-Seq data 1
pizzly - fast fusion detection using kallisto 2
PlasFlow Prediction of plasmid sequences in metagenomic contigs 1
Plot heatmap of OTU table (make_otu_heatmap) 2
Plot performance per cell in nanopore reads 1
Plot signals for nanopore reads 1
Plot tree 2
plotcon Plot quality of conservation of a sequence alignment 4
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 16
plotCoverage assesses the sequencing depth of BAM/CRAM files 16
plotEnrichment plots read/fragment coverage over sets of regions 12
plotFingerprint plots profiles of BAM files; useful for assessing ChIP signal strength 16
plotHeatmap creates a heatmap for score distributions across genomic regions 17
plotorf Plot potential open reading frames 5
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 16
plotProfile creates a profile plot for score distributions across genomic regions 16
Plotting of methylated regions 1
Plotting tool for multiple series and graph types 4
Poisson two-sample test 1
polydot Displays all-against-all dotplots of a set of sequences 4
Population Complexity : Evaluate possible numbers of ancestral populations 1
Porechop adapter trimmer for Oxford Nanopore reads 1
Pout2mzid add Percolator scoring to mzIdentML 1
Pre.cluster Remove sequences due to pyrosequencing errors 5
PrecursorIonSelector PrecursorIonSelector 3
PrecursorMassCorrector Corrects the precursor entries of MS/MS spectra, by using MS1 information. 4
Predict Metagenome based on the abundance of OTUs and a functional database 2
preg Regular expression search of a protein sequence 5
Prepare Input : Filter and convert to the format needed for these tools 1
Prepare ligand Tool to prepare ligand for Autodock Vina 1
Prepare receptor Tool to prepare receptor for Autodock Vina 1
Preprocess raw feature vectors into standardized datasets 2
Preprocessing 3
prettyplot Displays aligned sequences, with colouring and boxing 4
prettyseq Output sequence with translated ranges 4
Primer.design identify sequence fragments that are specific to particular OTUs 5
primersearch Searches DNA sequences for matches with primer pairs 4
Principal Component Analysis 2
PRINSEQ to process quality of sequences 3
Print Reads on BAM files 4
ProbMetab Tool Wrapper function for ProbMetab R package. 3
proFIA Preprocessing of FIA-HRMS data 4
Profile Annotations for a set of genomic intervals 2
Prokka Prokaryotic genome annotation 5
Promoter 2.0 Find eukaryotic PolII promoters in DNA sequences 4
Protease prediction based on cleavage sites 3
Protein Database Downloader 2
Protein Prophet Calculate Protein Prophet statistics on search results 1
ProteinInference Protein inference based on the number of identified peptides. 3
ProteinQuantifier Compute peptide and protein abundances 3
ProteinResolver protein inference 3
PSMFeatureExtractor Computes extra features for each input PSM. 1
psortb Determines sub-cellular localisation of bacterial/archaeal protein sequences 4
PTModel Trains a model for the prediction of proteotypic peptides from a training set. 3
PTPredict predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel 3
PubChem Assay Downloader as canonical SMILES 1
PubChem Download as canonical SMILES 1
PureCLIP - HMM based peak caller designed for eCLIP/iCLIP data 1
pyGenomeTracks plot genomic data tracks 2
QCCalculator Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. 3
QCEmbedder Attaches a table or an image to a given qc parameter. 2
QCExporter Will extract several qp from several run/sets in a tabular format. 2
QCExtractor Extracts a table attachment to a given qc parameter. 2
QCImporter Imports tables with quality control parameters into qcml files. 2
QCMerger Merges two qcml files together. 3
QCShrinker This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. 2
Quality format converter (ASCII-Numeric) 4
Quality Metrics Metrics and graphics to check the quality of the data 5
QualityScoreDistribution chart quality score distribution 11
QuanTP Correlation between protein and transcript abundances 1
Quast Genome assembly Quality 5
Query Tabular using sqlite sql 8
RaceID Race ID pipeline for single-cell RNA analysis 1
RaceID differential gene expression analysis Identify differentially regulated genes 1
RaceID3 performs single-cell RNA clustering and trajectory analysis 1
Racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 1
RandomBed generate random intervals in a genome 18
Rank Pathways : Assess the impact of a gene set on KEGG pathways 1
Rank Terms : Assess the enrichment/depletion of a gene set for GO terms 1
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 5
RAxML : construct a maximum-likelihood phylogenetic tree 1
RCAS - RNA Centric Annotation System 2
Re-align with SRMA 1
Reactivity Calculation calculates structural reactivity on each nucleotide based on RT stop counts from the Get RT Stop Counts module 1
Read Distribution calculates how mapped reads were distributed over genome feature 11
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 9
Read GC determines GC% and read count 9
Read length statistics from a set of FAST5 files 1
Read NVC to check the nucleotide composition bias 9
Read Quality determines Phred quality score 9
Realigner Target Creator for use in local realignment 4
Rebase GFF3 features against parent features 2
Reduce a HUMAnN2 generated table 2
Reduce Reads in BAM files 4
Regex Replace Regular Expression replacement using the Python re module 2
Regroup a HUMAnN2 generated table by features 2
Reheader copy SAM/BAM header between datasets 2
ReldistBed calculate the distribution of relative distances 17
Remarkable Intervals : Find high-scoring runs of SNPs 1
Remove 3'-end nts from FASTQ 2
Remove beginning of a file 1
Remove columns by heading 1
Remove counterions and fragments 1
Remove counterions and fragments 1
Remove duplicated molecules 1
Remove protonation state of every atom 1
Remove sequencing artifacts 5
Remove small molecules 1
Remove spurious crosslinking events 2
Remove Unwanted Variation from RNA-seq data 1
Remove.dists Removes distances from a phylip or column file 5
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 5
Remove.lineage Picks by taxon 5
Remove.otulabels Removes OTU labels 4
Remove.otus Removes OTUs from various file formats 5
Remove.rare Remove rare OTUs 5
Remove.seqs Remove sequences by name 5
remuRNA Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation 1
Rename features of a HUMAnN2 generated table 2
Rename sequences 5
Rename.seqs Rename sequences by concatenating the group name 3
Renormalize a HUMAnN2 generated table 2
Reorder individuals : exchange rows in the above picture 1
ReorderSam reorder reads to match ordering in reference sequences 14
Replace parts of text 6
Replace chromosome names in a tabular dataset using a mapping table 1
Replace column by values which are defined in a convert file 1
Replace Text in a specific column 6
Replace Text in entire line 6
ReplaceSamHeader replace header in a SAM/BAM dataset 14
Resize coordinate window of GFF data 3
Restore Attributes : Fill in missing properties for a gd_snp or gd_genotype dataset 1
Retrieve a run report 1
Retrieve an analysis report 1
Retrieve ENA data (other than taxon and project) 1
Retrieve ENA taxon data 1
Retrieve JBrowse for an organism, from Apollo 1
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 11
RevertSam revert SAM/BAM datasets to a previous state 11
revseq Reverse and complement a sequence 5
RmDup remove PCR duplicates 8
RNA fragment size calculates the fragment size for each gene/transcript 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 11
RNA Structure Prediction predict RNA structures with or without experimental constraints from the Reactivity Calculation module 1
RNA/DNA converter 5
RNA2Dfold explore structure space between two reference structures 1
RNAaliduplex find binding sites of two RNA alignments 1
RNAalifold Calculate minimum free energy secondary structures and partition function on a multiple alignment file 2
RNABOB Fast Pattern searching for RNA secondary structures 1
RNAcode Analyze the protein coding potential in MSA. 2
RNAcofold Calculate secondary structures of two RNAs with dimerization 1
RNAcommender genome-wide recommendation of RNA-protein interactions 2
RNAdistance Calculate distance between secondary structures of two RNAs 1
RNAduplex Compute the structure upon hybridization of two RNA strands 1
RNAeval Calculate energy of RNA sequences with given secondary structure 1
RNAfold Calculate minimum free energy secondary structures and partition function of RNAs 4
RNAheat Calculate energies of RNA in a temperature range 1
RNAinverse Calculate RNA sequence from secondary structure 1
RNALalifold Calculate locally stable secondary structures for a set of aligned RNAs 1
RNALfold calculates locally stable secondary structures of RNA 1
RNALfoldz calculates locally stable secondary structures of RNA 1
RNApaln RNA alignment based on sequence base pairing propensities 1
RNApdist Calculate distances between thermodynamic RNA secondary structure ensembles 1
RNAPKplex predicts RNA secondary structures including pseudoknots 1
RNAplex Find targets of a query RNA 1
RNAplot Draw RNA Secondary Structures 1
RNASeq samples quality check for transcript quantification 11
RNAshapes RNA Secondary structure prediction 2
RNAsnoop Find targets of a query H/ACA snoRNA 1
RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs 1
rnaSPAdes assembler for RNA-Seq data 4
RNAsubopt Calculates suboptimal secondary structures of RNAs 1
RNAup Calculate the thermodynamics of RNA-RNA interactions 1
RNAz predicting structurally conserved and thermodynamically stable RNA secondary structures 3
RnBeads Performs RnBeads analysis for the selected set of 1
RNPxl Tool for RNP cross linking experiment analysis. 2
RNPxlSearch Annotate RNA to peptide crosslinks in MS/MS spectra. 2
RNPxlXICFilter Remove MS2 spectra from treatment based on the fold change between control and treatment. 3
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 2
RPKM Count calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 6
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 11
RSEM calculate expression RNA-Seq by Expectation-Maximization 1
RSEM prepare reference 1
RSEM trinity fasta to gene map extract transcript to gene map from trinity 2
RTEvaluation Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. 3
RTModel Trains a model for the retention time prediction of peptides from a training set. 3
RTPredict Predicts retention times for peptides using a model trained by RTModel. 3
rtsne 1
Run a core set of QIIME diversity analyses (core_diversity_analyses) 3
Run join_paired_ends on multiple files (multiple_join_paired_ends) 2
Run split_libraries_fastq on multiple files (multiple_split_libraries_fastq) 2
RXLR Motifs Find RXLR Effectors of Plant Pathogenic Oomycetes 4
Sailfish transcript quantification from RNA-seq data 4
Salmon Transcript Quantification from RNA-seq data 5
Salmonella Subtyping 1
SAM-to-BAM convert SAM to BAM 11
SAM/BAM Alignment Summary Metrics 3
SAM/BAM GC Bias Metrics 3
SAM/BAM Hybrid Selection Metrics for targeted resequencing data 3
Sample SNPs : Select a specified number of SNPs, uniformly spaced 1
Sample_Subset Filter W4M data by sample class 5
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 14
Scatterplot of two numeric columns 5
Scatterplot w ggplot2 2
scPipe - preprocessing pipeline for single cell RNA-seq 1
Screen.seqs Screen sequences 5
SDF to CML 2
SDF to Fingerprint extract fingerprints from sdf files metadata 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Search ENA data given a query 1
Search engine output to Pin converter to create Percolator input files 1
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 12
Search in textfiles (grep) 6
Secure Hash / Message Digest on a dataset 1
SeedListGenerator Generates seed lists for feature detection. 2
segemehl based short read aligner 2
segmentation-fold RNA-Folding including predefined segments including K-turns 5
Select lines that match an expression 1
Select first lines from a dataset (head) 6
Select first lines from a dataset 1
Select high quality segments 3
Select last lines from a dataset (tail) 6
Select last lines from a dataset 1
Select random lines from a file 2
Select Variants from VCF files 4
SemanticValidator SemanticValidator for semantically validating certain XML files. 2
Sens.spec Determine the quality of OTU assignment 5
Separate pgSnp alleles into columns 1
Seq.error assess error rates in sequencing data 5
seqmatchall All-against-all comparison of a set of sequences 4
seqret Reads and writes sequences 5
seqtk_comp get the nucleotide composition of FASTA/Q 3
seqtk_cutN cut sequence at long N 3
seqtk_dropse drop unpaired from interleaved Paired End FASTA/Q 3
seqtk_fqchk fastq QC (base/quality summary) 3
seqtk_hety regional heterozygosity 3
seqtk_listhet extract the position of each het 3
seqtk_mergefa merge two FASTA/Q files 3
seqtk_mergepe interleave two unpaired FASTA/Q files for a paired-end file 3
seqtk_mutfa point mutate FASTA at specified positions 3
seqtk_randbase choose a random base from hets 3
seqtk_sample random subsample of fasta or fastq sequences 3
seqtk_seq common transformation of FASTA/Q 3
seqtk_subseq extract subsequences from FASTA/Q files 3
seqtk_trimfq trim FASTQ using the Phred algorithm 3
Sequence composition Count bases or amino-acids 3
Sequence converter for various sequence formats 1
Sequence Logo generator for fasta (eg Clustal alignments) 3
Sequence partition all-in-one Load, partition, and annotate FAST[AQ] sequences 2
SequenceCoverageCalculator Prints information about idXML files. 2
Seurat - toolkit for exploration of single-cell RNA-seq data 1
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Shape alignment against a database of molecules (Shape-it) 1
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
Shovill Faster SPAdes assembly of Illumina reads 2
Show nucleotide distribution in nanopore sequencing reads 1
Show quality score distribution in nanopore sequencing reads 1
showfeat Show features of a sequence 4
ShuffleBed randomly redistrubute intervals in a genome 18
shuffleseq Shuffles a set of sequences maintaining composition 4
SICER Statistical approach for the Identification of ChIP-Enriched Regions 2
Sickle windowed adaptive trimming of FASTQ data 5
SIFT predictions of functional sites 1
sigcleave Reports protein signal cleavage sites 4
SignalP 3.0 Find signal peptides in protein sequences 3
Similarity Search of fingerprint data sets 2
SimpleSearchEngine Annotates MS/MS spectra using SimpleSearchEngine. 2
Simulate Illumina runs 1
SiriusAdapter Tool for metabolite identification using single and tandem mass spectrometry 1
sirna Finds siRNA duplexes in mRNA 5
sixpack Display a DNA sequence with 6-frame translation and ORFs 5
skipseq Reads and writes sequences, skipping first few 4
Slice BAM by genomic regions 6
Slice VCF to get data from selected regions 2
SlopBed adjust the size of intervals 18
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
Smooth data with a running window 1
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 1
snippy-core Combine multiple Snippy outputs into a core SNP alignment 1
SnpEff Variant effect and annotation 15
SnpEff Available Databases 11
SnpEff build: database from Genbank or GFF record 6
SnpEff chromosome-info: list chromosome names/lengths 3
SnpEff Download Download a new database 15
SnpEff Ensembl CDS Report Variant coding sequence changes for SnpEffects 1
SnpEff to Peptide fasta to create a Search DB fasta for variant SAP peptides 1
snpFreq significant SNPs in case-control data 3
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift dbNSFP Add Annotations from dbNSFP or similar annotation DBs 4
SnpSift dbNSFP Add Annotations from dbNSFP and similar annotation DBs 2
SnpSift Extract Fields from a VCF file inot 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 9
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for Vcf specification compliance 7
SOPRA with prebuilt contigs for Illumina libraries 1
Sort BAM dataset 8
Sort data in ascending or descending order 6
Sort data in ascending or descending order 2
Sort a row according to their columns 6
Sort Column Order by heading 1
Sort.seqs put sequences in different files in the same order 5
SortBED order the intervals 17
SortSam sort SAM/BAM dataset 11
SpacingBed reports the distances between features 13
SPAdes genome assembler for regular and single-cell projects 10
Sparse Matrix Functions for manipulating 2-D Scipy sparse numeric data 2
Species tree generator from a list of species using the ETE Toolkit 1
Specify Individuals : Define a collection of individuals from a gd_snp dataset 1
SpecLibCreator Creates an MSP formatted spectral library. 2
SpecLibSearcher Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. 2
SpectraFilterBernNorm Applies thresholdfilter to peak spectra. 3
SpectraFilterMarkerMower Applies thresholdfilter to peak spectra. 3
SpectraFilterNLargest Applies thresholdfilter to peak spectra. 4
SpectraFilterNormalizer Normalizes intensity of peak spectra. 4
SpectraFilterParentPeakMower Applies thresholdfilter to peak spectra. 3
SpectraFilterScaler Applies thresholdfilter to peak spectra. 3
SpectraFilterSqrtMower Applies thresholdfilter to peak spectra. 3
SpectraFilterThresholdMower Applies thresholdfilter to peak spectra. 4
SpectraFilterWindowMower Applies thresholdfilter to peak spectra. 3
SpectraMerger Merges spectra (each MS level separately), increasing S/N ratios. 4
SpectraSTSearchAdapter Interface to the SEARCH Mode of the SpectraST executable 2
Spectrophores(TM) search: similarity search based on 1D chemical features 1
Split BAM datasets on variety of attributes 4
Split BAM dataset on readgroups 3
Split a HUMAnN2 generated table 2
Split fastq libraries to performs demultiplexing of Fastq sequence data (split_libraries_fastq) 2
Split file according to the values of a column 2
Split libraries according to barcodes specified in mapping file (split_libraries) 2
Split MAF blocks by Species 1
Split stratified table 1
Split.abund Separate sequences into rare and abundant groups 5
Split.groups Generates a fasta file for each group 5
SplitFasta 2
splitter Split a sequence into (overlapping) smaller sequences 4
SQLite to tabular for SQL query 4
SSAKE short DNA sequences assembler 1
ssHMM - RNA sequence-structure motif finder 1
Stacks: assemble read pairs by locus run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers 3
Stacks: cstacks build a catalogue of loci 4
Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 4
Stacks: genotypes analyse haplotypes or genotypes in a genetic cross ('genotypes' program) 3
Stacks: populations analyze a population of individual samples ('populations' program) 3
Stacks: process radtags the Stacks demultiplexing script 3
Stacks: pstacks find stacks from short reads mapped to a reference genome 3
Stacks: reference map the Stacks pipeline with a reference genome (ref_map.pl) 3
Stacks: rxstacks make corrections to genotype and haplotype calls 3
Stacks: sstacks match stacks to a catalog 3
Stacks: ustacks align short reads into stacks 3
STAR-Fusion detect fusion genes in RNA-Seq data 4
Statistical hypothesis testing 2
Stats generate statistics for BAM dataset 5
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 13
StringTie merge transcripts 7
Strip-it extracts predefined scaffolds from molecules 1
Structure using multi-locus genotype data to investigate population structure 3
Structure to GSPAN 2
Sub-sample sequences files e.g. to reduce coverage 4
Sub.sample Create a sub sample 5
Subset columns from a VCF dataset 2
Substructure Search of fingerprint data sets 1
Subtract the intervals of two datasets Filtering 7
Subtract Whole Dataset from another dataset 3
SubtractBed remove intervals based on overlaps 17
Summarize taxa and store results in a new table or appended to an existing mapping file (summarize_taxa) 2
Summarize taxonomy 1
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 5
Summary.seqs Summarize the quality of sequences 5
Summary.shared Summary of calculator values for OTUs 4
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 4
Support vector machines (SVMs) for classification 2
Support vector machines (SVMs) for classification 1
SvmTheoreticalSpectrumGeneratorTrainer Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator 3
syco Synonymous codon usage Gribskov statistic plot 4
T Test for Two Samples 2
T-Coffee multiple sequence alignment 2
Tabular to FASTQ converter 4
Tabular-to-FASTA converts tabular file to FASTA format 2
tac reverse a file (reverse cat) 6
Tag pileup frequency 2
TagBed tag BAM alignments based on overlaps with interval files 17
TargetedFileConverter Converts different transition files for targeted proteomics / metabolomics analysis. 2
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 3
Taylor-Butina Clustering of molecular fingerprints 2
tcode Fickett TESTCODE statistic to identify protein-coding DNA 4
Text reformatting with awk 6
Text transformation with sed 6
TextExporter Exports various XML formats to a text file. 3
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
Thermo RAW file converter (beta) 1
Thread nucleotides onto a protein alignment (back-translation) Gives a codon aware alignment 4
TICCalculator Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). 2
Tiling (running window) 1
tmap Displays membrane spanning regions 5
TMHMM 2.0 Find transmembrane domains in protein sequences 4
TOFCalibration Applies time of flight calibration. 3
TopHat Gapped-read mapper for RNA-seq data 12
Tophat Fusion Post post-processing to identify fusion genes 1
TopPerc Facilitate input to Percolator and reintegrate. 2
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 5
TransDecoder Find coding regions within transcripts 4
transeq Translate nucleic acid sequences 5
Transform real vector graphs to sparse vectors 1
Transformation Transforms the dataMatrix intensity values 4
TransformationEvaluation Applies a transformation to a range of values 2
Translate BED Sequences 3 frame translation of BED augmented with a sequence column 1
Translate nucleotides to amino acids 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
TreeBeST best Generate a phylogenetic tree using CDS alignment and species tree 1
TreeBeST best Generate a phylogenetic tree using CDS alignment and species tree 1
Trim leading or trailing characters 1
Trim Galore! Quality and adapter trimmer of reads 8
Trim putative adapter sequence 1
Trim sequences 6
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 4
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 13
trimseq Trim ambiguous bits off the ends of sequences 4
Trinity de novo assembly of RNA-Seq data 13
tRNA and tmRNA prediction (Aragorn) 3
tRNA prediction (tRNAscan) 3
twoBitToFa Convert all or part of .2bit file to fasta 3
twofeat Finds neighbouring pairs of features in sequences 4
UMI-tools count performs quantification of UMIs from BAM files 3
UMI-tools deduplicate Extract UMI from fastq files 1
UMI-tools extract Extract UMI from fastq files 5
UMI-tools group Extract UMI from fastq files 2
UMI-tools whitelist Extract cell barcodes from FASTQ files 2
Unfold columns from a table 6
Unified Genotyper SNP and indel caller 4
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 2
UniProt download proteome as XML or fasta 3
UniProt ID mapping and retrieval 3
Unique occurrences of each record 6
Unique occurrences of each record 2
Unique lines assuming sorted input file 6
Unique.seqs Return unique sequences 5
Univariate Univariate statistics 6
Unpack pathway abundances to show genes included 1
Upload File from your computer 2
UpSet diagram of intersection of genomic regions or list sets 1
VALET to detect mis-assemblies in metagenomic assemblies 1
Validate Variants 3
ValidateSamFile assess validity of SAM/BAM dataset 11
Variant Annotator 4
Variant Annotator process variant counts 2
Variant Filtration on VCF files 4
Variant Recalibrator 4
VarScan for variant detection 3
VarScan copynumber Determine relative tumor copy number from tumor-normal pileups 2
VarScan mpileup mutation caller for targeted, exome, and whole-genome resequencing 3
VarScan Somatic somatic mutation caller for cancer genomics 3
VCF to MAF Custom Track for display at UCSC 1
VCF to pgSnp Convert from VCF to pgSnp format 2
VCF-BEDintersect: Intersect VCF and BED datasets 6
VCF-VCFintersect: Intersect two VCF datasets 7
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 7
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 6
VCFannotate: Intersect VCF records with BED annotations 6
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 7
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 6
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 7
VCFcommonSamples: Output records belonging to samples common between two datasets 6
VCFdistance: Calculate distance to the nearest variant 6
VCFfilter: filter VCF data in a variety of attributes 6
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 7
VCFgenotypes: Convert numerical representation of genotypes to allelic 6
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 6
VCFleftAlign: Left-align indels and complex variants in VCF dataset 6
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 7
VCFselectsamples: Select samples from a VCF dataset 7
VCFsort: Sort VCF dataset by coordinate 5
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 8
vectorstrip Strips out DNA between a pair of vector sequences 4
Vegan Diversity index 3
Vegan Fisher Alpha index 3
Vegan Rarefaction curve and statistics 3
velvetg Velvet sequence assembler for very short reads 4
velveth Prepare a dataset for the Velvet velvetg Assembler 4
Venn Generate Venn diagrams for groups 5
Venn Diagram from lists 5
Violin plot w ggplot2 2
Visualisation of compounds 1
Visualize the optimal scoring subnetwork 1
Visualize with Krona Visualise any hierarchical data 2
VSearch alignment Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch chimera detection Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch clustering Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch dereplication Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch masking Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch search Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch shuffling Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch sorting Chimeric sequence detection Sequence clustering Sequence masking 6
VT normalize normalizes variants in a VCF file 1
water Smith-Waterman local alignment 4
Wavelet variance using Discrete Wavelet Transfoms 2
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1
WindowBed find overlapping intervals within a window around an interval 17
wobble Wobble base plot 4
WoLF PSORT Eukaryote protein subcellular localization prediction 3
wordcount Counts words of a specified size in a DNA sequence 4
wordmatch Finds all exact matches of a given size between 2 sequences 4
WTDBG De novo assembler AND consensuser for long noisy sequences 1
X!Tandem MSMS Search Run an X!Tandem Search - test 1
X!Tandem MSMS Search Run an X!Tandem Search 1
xcms adjustRtime (retcor) Retention Time Correction 9
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 10
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 12
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 4
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 10
xcms process history Create a summary of XCMS analysis 7
XFDR Calculates false discovery rate estimates on crosslink identifications 1
XMLValidator Validates XML files against an XSD schema. 2
XPath compute xpath expressions on XML data 2
XTandemAdapter Annotates MS/MS spectra using X! Tandem. 4
zerone 1