1153 tool(s) found

Tool Description Topics Available version(s)
AEGeAn CanonGFF3 pre-process GFF3 files, removing all features not directly related to protein-coding genes Genome annotation 1
2DNMR_Annotation Annotation of complex mixture bidimensional NMR spectra 2
Abundance index computation across species, sites and years 1
Add column to an existing dataset Editing 2
Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas] 3
Add protein features [UniProt, Human, Mouse, Rat] 1
Add protein features [neXtProt] 3
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
Advanced Cut columns from a table (cut) 8
Advanced restitution: 'Point fixe' protocol from Animal Detection on Acoustic Recordings 1
Advanced restitution: 'Routier'or 'Pedestre' protocols from Animal Detection on Acoustic Recordings 1
AEGeAn GAEVAL compute coverage and integrity scores for gene models using transcript alignments. Genome annotation 1
AEGeAn LocusPocus calculate locus coordinates for the given gene annotation Genome annotation 1
AEGeAn ParsEval compare two sets of gene annotations for the same sequence. Genome annotation 1
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 12
Align sequences using a variety of alignment methods (align_seqs) 2
Align.check Calculate the number of potentially misaligned bases 6
Align.seqs Align sequences to a template alignment 5
Amova Analysis of molecular variance 5
Analytic correlation filtration : Detect analytic correlation among data and remove them. 1
Analyze statistical significance of sample groupings using distance matrices (compare_categories) 2
Annotate a VCF dataset with custom filters 1
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
annotateMyIDs annotate a generic set of identifiers 8
Anosim Non-parametric multivariate analysis of changes in community structure 5
Anova N-way anova. With ou Without interactions 3
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 5
Arithmetic Operations on tables 2
ASCA Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block 1
Assign taxonomy to each sequence (assign_taxonomy) 2
Augustus gene prediction for prokaryotic and eukaryotic genomes 7
Autocorrelation test check for temporal autocorrelation in the residuals 1
backtranseq Back translate a protein sequence 7
BAM filter Removes reads from a BAM file based on criteria 4
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 7
BAM-to-SAM convert BAM to SAM 5
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 7
bamCompare normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them 17
bamCoverage generates a coverage bigWig file from a given BAM or CRAM file 18
BamLeftAlign indels in BAM datasets 13
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 17
banana Bending and curvature plot in B-DNA 5
Bandage Image visualize de novo assembly graphs 6
Bandage Info determine statistics of de novo assembly graphs 5
bank_inhouse search by accurate mass (and by Retention time) on a local bank 1
Barcode Splitter 4
barrnap Locate ribosomal RNA's in a fasta file. (GFF output) 3
Base Coverage of all intervals Quantification 4
Batch_correction Corrects intensities for signal drift and batch-effects 4
bcftools annotate Annotate and edit VCF/BCF files 6
bcftools call SNP/indel variant calling from VCF/BCF 8
bcftools cnv Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR) 9
bcftools color-chrs plugin Color shared chromosomal segments, requires phased GTs 3
bcftools concat Concatenate or combine VCF/BCF files 6
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 9
bcftools convert from vcf Converts VCF/BCF to IMPUTE2/SHAPEIT formats 6
bcftools convert to vcf Converts other formats to VCF/BCFk 6
bcftools csq Haplotype aware consequence predictor 7
bcftools filter Apply fixed-threshold filters 6
bcftools frameshifts plugin Annotate frameshift indels 3
bcftools gtcheck Check sample identity 6
bcftools isec Create intersections, unions and complements of VCF files 6
bcftools merge Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file 7
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 6
bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows 9
bcftools query Extracts fields from VCF/BCF file and prints them in user-defined format 7
bcftools reheader Modify header of VCF/BCF files, change sample names 6
bcftools roh HMM model for detecting runs of homo/autozygosity 6
bcftools stats Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats 7
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 2
BedCov calculate read depth for a set of genomic intervals 5
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
Between-table Correlation Correlation table between two tables and graphic representation 2
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 17
Bih4MaConDa : Utility to detect potential contaminants in your peak list based on MaConDa database 2
Bin.seqs Order Sequences by OTU 5
Biological theme comparison (Human, Mouse, Rat)[clusterProfiler] 1
Biom.info create shared and taxonomy files from biom 2
biosed Replace or delete sequence sections 5
Biosigner Molecular signature discovery from omics data 2
biosyntheticSPAdes biosynthetic gene cluster assembly 4
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Bowtie2 - map reads against reference genome 19
btwisted Calculates the twisting in a B-DNA sequence 5
Build a UPGMA tree comparing samples (upgma_cluster) 2
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 12
Build Protein interaction network [BioGRID, BioPlex, HuMAP] 1
Build tissue-specific expression dataset [Human Protein Atlas](no input required) 2
Bundle Collection Download a collection of files 2
Busco assess genome assembly and annotation completeness 12
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) 2
Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables (beta_diversity) 2
Calculate community metrics calculate community metrics from abundance data 4
Calculate metrics for classification performance 12
Calculate metrics for regression performance 11
Calculate presence absence table calculate presence absence table from observation data 4
Call variants with LoFreq 6
CalMD recalculate MD/NM tags 5
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 9
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 9
Canonical Correlation Analysis 1
cast expand combinations of variables:values to columnar format 1
Categorize by collapsing hierarchical data to a specified functional level 2
Change Case of selected columns 2
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 5
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 2
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 5
Chimera.bellerophon Find putative chimeras using bellerophon 5
Chimera.ccode Find putative chimeras using ccode 6
Chimera.check Find putative chimeras using chimeraCheck 5
Chimera.perseus Find putative chimeras using chimeraCheck 6
Chimera.pintail Find putative chimeras using pintail 5
Chimera.slayer Find putative chimeras using slayer 5
Chimera.uchime Find putative chimeras using uchime 5
Chimera.vsearch find potential chimeric sequences using vsearch 4
chips Codon usage statistics 5
Chop.seqs Trim sequences to a specified length 6
Circos visualizes data in a circular layout Visualisation 11
Circos: Alignments to links reformats alignment files to prepare for Circos Parsing 10
Circos: bigWig to Scatter reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots Conversion 10
Circos: Bundle Links reduce numbers of links in datasets before plotting Aggregation 10
Circos: Interval to Circos Text Labels reformats interval files to prepare for Circos text labels Conversion 10
Circos: Interval to Tiles reformats interval files to prepare for Circos tile plots Conversion 10
Circos: Link Density Track reduce links to a density plot Aggregation 10
Circos: Resample 1/2D data reduce numbers of points in a dataset before plotting Aggregation 10
Circos: Stack bigWigs as Histogram reformats for use in Circos stacked histogram plots Formatting 6
Circos: Table viewer easily creates circos plots from tabular data Visualisation 10
cirdna Draws circular maps of DNA constructs 5
Classify.otu Assign sequences to taxonomy 5
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 5
Classify.tree Get a consensus taxonomy for each node on a tree 5
CleanSam perform SAM/BAM grooming 14
Clearcut Generate a tree using relaxed neighbor joining 5
Clip adapter sequences 6
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 7
Closed-reference OTU picking Shotgun UniFrac workflow (pick_closed_reference_otus) 2
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 4
Cluster.classic Assign sequences to OTUs (Dotur implementation) 5
Cluster.fragments Group sequences that are part of a larger sequence 5
Cluster.split Assign sequences to OTUs and split large matrices 5
CML to SMILES 3
codcmp Codon usage table comparison 5
coderet Extract CDS, mRNA and translations from feature tables 5
Collapse sequences 3
Collapse Collection into single dataset in order of the collection 5
Collapse samples Collapse samples in a BIOM table and mapping file 1
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
Collect.shared Generate collector's curves for calculators on OTUs 5
Collect.single Generate collector's curves for OTUs 7
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 3
CollectInsertSizeMetrics plots distribution of insert sizes 14
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 14
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
Column arrange by header name 2
Column Join on Collections 5
Column Regex Find And Replace 4
Combine FASTA and QUAL into FASTQ Aggregation 5
Compare BIOM tables Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. 3
Compare two Datasets to find common or distinct rows Filtering 1
Complement intervals of a dataset Sequence coordinate conversion 5
compseq Count composition of dimer/trimer/etc words in a sequence 5
Compute an expression on every row 9
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) 21
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute functional profiles (Human, Mouse) [goProfiles] 2
Compute GLM on community data Compute a GLM of your choice on community data 3
Compute GLM on population data Compute a GLM of your choice on population data 3
Compute quality statistics 3
Compute sequence length 6
computeGCBias Determine the GC bias of your sequenced reads 18
computeMatrix prepares data for plotting a heatmap or a profile of given regions 17
Concatenate FASTA alignment by species 3
Concatenate two BED files Aggregation 5
Concatenate datasets tail-to-head Aggregation 1
Concatenate datasets tail-to-head (cat) 10
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
Convert delimiters to TAB 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert Biom datasets 1
Convert CSV to tabular 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to fai file 1
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert genome coordinates between assemblies and genomes 2
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert GTF to BED12 1
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to interval 2
Convert SAM to BAM without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 2
Convert tar to directory 2
Convert uncompressed BCF to BCF 1
Convert, Merge, Randomize BAM datasets and perform other transformations 5
Cooccurrence tests whether presence-absence patterns differ from chance 6
coronaSPAdes SARS-CoV-2 de novo genome assembler 4
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 17
Correlation for numeric columns 1
Count occurrences of each record 2
Count GFF Features 2
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 4
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 5
Create a plot from GLM data as temporal trend 2
Create assemblies with Unicycler Genome assembly 8
Create single interval as a new dataset 1
Create text file with recurring lines 8
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 5
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 8
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
cusp Create a codon usage table 5
CustomProDB Generate protein FASTAs from exosome or transcriptome data 2
Cut columns from a table Filtering 2
Cutadapt Remove adapter sequences from Fastq/Fasta Sequence editing 20
cutseq Removes a specified section from a sequence 5
dada2: assignTaxonomy and addSpecies Learn Error rates 6
dada2: dada Remove sequencing errors 6
dada2: filterAndTrim Filter and trim short read data 6
dada2: learnErrors Learn Error rates 6
dada2: makeSequenceTable construct a sequence table (analogous to OTU table) 6
dada2: mergePairs Merge denoised forward and reverse reads 6
dada2: plotComplexity Plot sequence complexity profile 6
dada2: plotQualityProfile plot a visual summary of the quality scores 6
dada2: removeBimeraDenovo Remove bimeras from collections of unique sequences 6
dada2: sequence counts 6
dan Calculates DNA RNA/DNA melting temperature 5
Data Fetch Query and retrieval 1
Datamash (operations on tabular data) 3
DAVID functional annotation for a list of genes 1
Degap.seqs Remove gap characters from sequences 5
degapseq Removes gap characters from sequences 5
Deletion Profile calculates the distributions of deleted nucleotides across reads 3
Describe samples and replicates 11
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 21
Determine_batch_correction to choose between linear, lowess and loess methods 4
Deunique.seqs Return all sequences 5
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 5
DEXSeq Determines differential exon usage from count tables 9
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 9
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 8
Diamond makedb Build database from a FASTA file Sequence alignment analysis 7
Diamond view generate formatted output from DAA files Sequence alignment analysis 5
DiffBind differential binding analysis of ChIP-Seq peak data 12
Differential expression analysis using a Trinity assembly 11
diffseq Find differences between nearly identical sequences 5
digest Protein proteolytic enzyme or reagent cleavage digest 5
Discriminant Analysis 12
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
dotmatcher Displays a thresholded dotplot of two sequences 5
dotpath Non-overlapping wordmatch dotplot of two sequences 5
dottup Displays a wordmatch dotplot of two sequences 5
Download and Extract Reads in BAM format from NCBI SRA 22
Download and Extract Reads in FASTA/Q format from NCBI SRA 18
Download and Generate Pileup Format from NCBI SRA 9
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
Draw nucleotides distribution chart 4
Draw quality score boxplot 4
Draw ROC plot on "Perform LDA" output 2
Draw Stacked Bar Plots for different categories and different criteria 1
dreg Regular expression search of a nucleotide sequence 7
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
eggNOG Mapper functional sequence annotation by orthology 7
einverted Finds DNA inverted repeats 5
ENA Upload tool 7
Enrichment analysis (Human, Mouse, Rat)[topGO] 2
Ensemble methods for classification and regression 12
epestfind Finds PEST motifs as potential proteolytic cleavage sites 5
equicktandem Finds tandem repeats 5
est2genome Align EST and genomic DNA sequences 5
Estimate temporal population evolution by species 2
Estimate temporal population variation by specialization group 3
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
etandem Looks for tandem repeats in a nucleotide sequence 5
Evaluate pairwise distances or compute affinity or kernel for sets of samples 12
Expected temporal trend of species abundance 1
Extract and cluster differentially expressed transcripts from a Trinity assembly 12
Extract element identifiers of a list collection 2
Extract features from GFF data 1
Extract MAF blocks given a set of genomic intervals 3
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
extractfeat Extract features from a sequence 5
extractseq Extract regions from a sequence 5
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 4
Fasta Statistics Display summary statistics for a fasta file. 5
FASTA Width formatter 3
FASTA-to-Tabular converter 3
FastaCLI Appends decoy sequences to FASTA files 5
Faster Download and Extract Reads in FASTQ format from NCBI SRA 12
fastp - fast all-in-one preprocessing for FASTQ files 8
FASTQ de-interlacer on paired end reads Splitting 5
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FASTQ interlacer on paired end reads Aggregation 6
FASTQ joiner on paired end reads Aggregation 7
FASTQ Masker by quality score Sequence masking 5
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads Splitting 6
FASTQ Summary Statistics by column Sequence assembly validation 4
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 6
FASTQ to Tabular converter Sequence conversion 5
FASTQ Trimmer by column Sequence trimming 5
Fastq.info Convert fastq to fasta and quality 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FASTQE visualize fastq files with emoji's 🧬😎 5
FastqToSam convert Fastq data into unaligned BAM 18
FASTTREE build maximum-likelihood phylogenetic trees Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
Feature Selection module, including univariate filter selection methods and recursive feature elimination algorithm 12
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
Fetch closest non-overlapping feature for every interval Filtering 3
fgsea - fast preranked gene set enrichment analysis 3
Filter data on any column using simple expressions Formatting 2
Filter BAM datasets on a variety of attributes 5
Filter by keywords and/or numerical value 4
Filter by quality Filtering 6
Filter Combined Transcripts using tracking file 1
Filter FASTA on the headers and/or the sequences 4
Filter fasta to remove sequences based on input criteria (filter_fasta) 2
Filter FASTQ reads by quality score and length Filtering 4
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 2
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter 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 SAM on bitwise flag values 1
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 5
Filter sequence alignment by removing highly variable regions (filter_alignment) 2
Filter sequences by ID from a tabular file 5
Filter sequences by length Filtering 6
Filter species with rare and low abundances 2
Filter taxa from an OTU table (filter_taxa_from_otu_table) 2
Filter with SortMeRNA of ribosomal RNAs in metatranscriptomic data 6
Filter.seqs removes columns from alignments 5
Filter.shared remove OTUs based on various critieria 6
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 14
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
Flagstat tabulate descriptive stats for BAM datset 8
Flight curve compute the regional expected pattern of abundance 1
Flye assembly of long and error-prone reads Genome assembly 7
Format tree and trait tables 2
Format Fastq sequences and barcode data (extract_barcodes) 2
Format MetaPhlAn2 output for Krona 2
FPKM Count calculates raw read count, FPM, and FPKM for each gene 5
freak Residue/base frequency table or plot 5
FreeBayes bayesian genetic variant detector 13
FROGS Abundance normalisation Normalise OTUs abundance. Standardisation and normalisation 4
FROGS Affiliation Filters Filters OTUs on several affiliation criteria. 2
FROGS Affiliation OTU Taxonomic affiliation of each OTU's seed by RDPtools and BLAST Taxonomic classification 4
FROGS Affiliation postprocess Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics Taxonomic classification 4
FROGS Affiliations stat Process some metrics on taxonomies. Taxonomic classification 4
FROGS BIOM to std BIOM Converts a FROGS BIOM in fully compatible BIOM. Formatting 4
FROGS BIOM to TSV Converts a BIOM file in TSV file. Formatting 4
FROGS Clustering swarm Single-linkage clustering on sequences Taxonomic classification 4
FROGS Clusters stat Process some metrics on clusters. Clustering 4
FROGS Demultiplex reads Attribute reads to samples in function of inner barcode. Classification 4
FROGS ITSx Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. Sequence trimming 4
FROGS OTU Filters Filters OTUs on several criteria. 2
FROGS Pre-process merging, denoising and dereplication. Filtering 4
FROGS Remove chimera Remove PCR chimera in each sample. Editing 4
FROGS Tree Reconstruction of phylogenetic tree Taxonomic classification 4
FROGS TSV_to_BIOM Converts a TSV file in a BIOM file. Formatting 4
FROGSSTAT DESeq2 Preprocess import a Phyloseq object and prepare it for DESeq2 differential abundance analysis 2
FROGSSTAT Phyloseq Alpha Diversity with richness plot Taxonomic classification 4
FROGSSTAT Phyloseq Beta Diversity distance matrix Taxonomic classification 4
FROGSSTAT Phyloseq Composition Visualisation with bar plot and composition plot Taxonomic classification 4
FROGSSTAT Phyloseq Import Data from 3 files: biomfile, samplefile, treefile Taxonomic classification 4
FROGSSTAT Phyloseq Multivariate Analysis Of Variance perform Multivariate Analysis of Variance (MANOVA) Taxonomic classification 4
FROGSSTAT Phyloseq Sample Clustering of samples using different linkage methods Taxonomic classification 4
FROGSSTAT Phyloseq Structure Visualisation with heatmap plot and ordination plot Taxonomic classification 4
FROGSTAT Deseq2 Visualisation to extract and visualise differentially abundant OTUs 2
Funannotate assembly clean 4
Funannotate compare annotations 4
Funannotate functional annotation 4
Funannotate predict annotation 5
fuzznuc Nucleic acid pattern search 6
fuzzpro Protein pattern search 5
fuzztran Protein pattern search after translation 5
g:Profiler tools for functional profiling of gene lists 1
garnier Predicts protein secondary structure 5
GC Skew calculates skew over genomic sequences Nucleic acid property calculation 10
GDAL addo builds or rebuilds overview images 2
GDAL Build VRT builds a VRT from a list of datasets 2
GDAL Informations lists information about a raster dataset 2
GDAL Merge mosaics a set of images 2
GDAL Translate converts raster data between different formats. 2
GDAL Warp image reprojection and warping utility 2
geecee Calculates fractional GC content of nucleic acid sequences 5
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 3
GEMINI amend Amend an already loaded GEMINI database. 4
GEMINI annotate the variants in an existing GEMINI database with additional information 6
GEMINI burden perform sample-wise gene-level burden calculations 3
GEMINI database info Retrieve information about tables, columns and annotation data stored in a GEMINI database 3
GEMINI fusions Identify somatic fusion genes from a GEMINI database 4
GEMINI gene_wise Custom genotype filtering by gene 4
GEMINI inheritance pattern based identification of candidate genes 1
GEMINI interactions Find genes among variants that are interacting partners 3
GEMINI load Loading a VCF file into GEMINI 6
GEMINI lof_sieve Filter LoF variants by transcript position and type 3
GEMINI pathways Map genes and variants to KEGG pathways 4
GEMINI qc Quality control tool 4
GEMINI query Querying the GEMINI database 4
GEMINI roh Identifying runs of homozygosity 4
GEMINI set_somatic Tag somatic mutations in a GEMINI database 4
GEMINI stats Compute useful variant statistics 3
GEMINI windower Conducting analyses on genome "windows" 3
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 10
Gene Body Coverage (Bigwig) Read coverage over gene body 10
Generalized linear models for classification and regression 11
Generate random samples with controlled size and complexity 12
Generate A Matrix for using PC and LDA 1
Generate gene to transcript map for Trinity assembly 10
Generate pileup from BAM dataset 3
Generate SuperTranscripts from a Trinity assembly 6
Generic_Filter Removes elements according to numerical or qualitative values 3
Genome annotation statistics 1
GenomeScope reference-free genome profiling 2
Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas] 2
Get flanks returns flanking region/s for every gene Sequence analysis 4
Get MS/MS observations in tissue/fluid [Peptide Atlas] 3
Get species occurrences data from GBIF, ALA, iNAT and others 1
Get unique peptide SRM-MRM method [Human SRM Atlas] 2
Get.communitytype description 5
Get.coremicrobiome fraction of OTUs for samples or abundances 6
Get.dists selects distances from a phylip or column file 5
Get.group group names from shared or from list and group 6
Get.groups Select groups 5
Get.label label names from list, sabund, or rabund file 5
Get.lineage Picks by taxon 6
Get.mimarkspackage creates a mimarks package form with your groups 5
Get.otulabels Selects OTU labels 6
Get.otulist Get otus for each distance in a otu list 5
Get.oturep Generate a fasta with a representative sequence for each OTU 5
Get.otus Get otus containing sequences from specified groups 5
Get.rabund Get rabund from a otu list or sabund 6
Get.relabund Calculate the relative abundance of each otu 5
Get.sabund Get sabund from a otu list or rabund 5
Get.seqs Picks sequences by name 5
Get.sharedseqs Get shared sequences at each distance from list and group 5
GetFastaBed use intervals to extract sequences from a FASTA file 20
getorf Finds and extracts open reading frames (ORFs) 5
GFF align 1
GFF-to-BED converter Conversion 2
GffCompare compare assembled transcripts to a reference annotation 4
gffread Filters and/or converts GFF3/GTF2 records 7
GMAJ Multiple Alignment Viewer 1
GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] 3
Golm Metabolome Database search spectrum : GC-MS Mass Spectral Database. 2
goseq tests for overrepresented gene categories Gene-set enrichment analysis 10
Group data by a column and perform aggregate operation on other columns. 4
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
HeatMap (clustering and visualization) 1
Heatmap Heatmap of the dataMatrix 2
Heatmap w ggplot 3
Heatmap.bin Generate a heatmap for OTUs 5
Heatmap.sim Generate a heatmap for pariwise similarity 5
heatmap2 4
helixturnhelix Report nucleic acid binding motifs 5
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 3
HISAT2 A fast and sensitive alignment program 18
Histogram of a numeric column 4
Histogram w ggplot2 4
HMDB bank downloader : get a specific metabolite bank (as Urine...) from HMDB web portal. 1
HMDB MS search search by masses on HMDB online LCMS bank 4
hmoment Hydrophobic moment calculation 5
Homoscedasticity and normality Checks the homogeneity of the variance and the normality of the distribution 1
Homova Homogeneity of molecular variance 5
HR2 formula find a chemical formula from a accurate mass 1
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
HUMAnN2 to profile presence/absence and abundance of microbial pathways and gene families 5
Hyperparameter Search performs hyperparameter optimization using various SearchCVs 11
HyPhy-aBSREL adaptive Branch Site Random Effects Likelihood 24
HyPhy-GARD Genetic Algorithm for Recombination Detection 23
ID choice Choosing a particular column in your metadata to be considered as Identifiers 2
ID Converter (Human, Mouse, Rat) 2
Identification Parameters Sets the identification parameters to be used in SearchGUI and PeptideShaker apps 5
IdxStats reports stats of the BAM index file 8
iep Calculates the isoelectric point of a protein 5
Illuminapairedend - Assembling pair-end reads Construct consensus reads from Illumina pair-end reads 3
InChI to MOL 3
Indicator Identify indicator "species" for nodes on a tree 5
Infer Experiment speculates how RNA-seq were configured 9
influx_si metabolic flux analysis 1
infoseq Displays some simple information about sequences 5
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 9
Insert indel qualities into a BAM file 3
Insertion Profile calculates the distribution of inserted nucleotides across reads 3
Intensity Check Statistical measures, number of missing values and mean fold change 2
InterProScan functional annotation 6
Intersect the intervals of two datasets Filtering 5
Intersect intervals find overlapping intervals in various ways 22
ISA to mzData Extract mzData files from an ISA dataset and output a collection of mzData dataset. 1
ISA to mzML Extract mzML files from an ISA dataset and output a collection of mzML dataset. 1
ISA to mzXML Extract mzXML files from an ISA dataset and output a collection of mzXML dataset. 1
ISA to netCDF Extract netCDF files from an ISA dataset and output a collection of netCDF dataset. 1
ISA to nmrML Extract nmrML files from an ISA dataset and output a collection of nmrML dataset. 1
ISA to W4M Convert ISA data type into W4M format 1
isochore Plots isochores in large DNA sequences 5
Isoplot: Generate plots from isocor output 2
Isotope Correction for mass spectrometry labeling experiments 1
ivar consensus Call consensus from aligned BAM file 5
ivar filtervariants Filter variants across replicates or multiple samples aligned using the same reference 5
ivar getmasked Detect primer mismatches and get primer indices for the amplicon to be masked 4
ivar removereads Remove reads from trimmed BAM file 8
ivar trim Trim reads in aligned BAM 9
ivar variants Call variants from aligned BAM file 6
JBrowse genome browser Map drawing Sequence visualisation 31
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance Conversion 30
jellyfish 1
Join two files 11
Join the intervals of two datasets side-by-side Aggregation 4
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
JQ process JSON 1
Junction Annotation compares detected splice junctions to reference gene model 9
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 9
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 6
Kallisto quant - quantify abundances of RNA-Seq transcripts 8
KEGG pathways mapping and coverage [PathView] 2
KEGG pathways mapping and visualization [PathView] 1
Kernel Canonical Correlation Analysis 2
Kernel Principal Component Analysis 2
KisSplice is a local transcriptome assembler for SNPs, indels and AS events 3
Kraken assign taxonomic labels to sequencing reads 8
Kraken-filter filter classification by confidence score 4
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 5
Kraken-translate convert taxonomy IDs to names 5
Krona pie chart from taxonomic profile 10
LAST-split finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). 4
LAST-train finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. 5
LASTal finds local alignments between query sequences, and reference sequences. 6
LASTdb prepares sequences for subsequent comparison and alignment using lastal. 5
LASTZ : align long sequences 7
LASTZ_D : estimate substitution scores matrix 5
LCMS matching Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. 3
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
Libshuff Cramer-von Mises tests communities for the same structure 5
limma Perform differential expression with limma-voom or limma-trend Differential gene expression profiling RNA-seq read count analysis 19
lindna Draws linear maps of DNA constructs 5
Line/Word/Character count of a dataset 1
Linear regression ajusted for autocorrelation in the residuals 1
Lipidmaps : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. 1
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
Local Contributions to Beta Diversity (LCBD) Computes a measure of beta diversity, SCBD and representations 1
Lofreq filter called variants posteriorly 4
MACS2 bdgbroadcall Call broad peaks from bedGraph output 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files 9
MACS2 bdgpeakcall Call peaks from bedGraph output 8
MACS2 callpeak Call peaks from alignment results 11
MACS2 filterdup Remove duplicate reads at the same position 8
MACS2 predictd Predict 'd' or fragment size from alignment results 8
MACS2 randsample Randomly sample number or percentage of total reads 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) 8
MAF Coverage Stats Alignment coverage information 3
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
MAF-convert read MAF-format alignments and write them in another format. 4
MAFFT Multiple alignment program for amino acid or nucleotide sequences 7
MAFFT add Align a sequence,alignment or fragments to an existing alignment. 4
Make Design Assign groups to Sets 5
Make OTU table Make an OTU table from an OTU map and a taxonomy assignment file 1
Make phylogeny (make_phylogeny) 2
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 6
Make.fastq Convert fasta and quality to fastq 6
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 6
Make.lookup allows you to create custom lookup files for use with shhh.flows 5
Make.shared Make a shared file from a list and a group 5
Make.sra creates the necessary files for a NCBI submission 5
Maker genome annotation pipeline 9
Manipulate FASTQ reads on various attributes Sequence conversion 4
Mantel Mantel correlation coefficient between two matrices. 5
Map annotation ids on a Maker annotation 6
Map with BWA - map short reads (< 100 bp) against reference genome 11
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 13
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences Sequence alignment 18
MapBed apply a function to a column for each overlapping interval 21
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 15
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 14
marscan Finds MAR/SAR sites in nucleic sequences 5
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
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
matcher Finds the best local alignments between two sequences 5
MeanQualityByCycle chart distribution of base qualities 14
medaka consensus pipeline Assembly polishing via neural networks 9
medaka consensus tool Assembly polishing via neural networks 9
medaka variant tool Probability decoding 12
megamerger Merge two large overlapping nucleic acid sequences 5
melt collapse combinations of variables:values to single lines 1
Merge the overlapping intervals of a dataset Sequence merging 4
Merge BAM Files merges BAM files together 3
Merge Columns together 4
Merge.count Merge count tables 2
Merge.files Merge data 5
Merge.groups Merge groups in a shared file 5
Merge.sfffiles Merge SFF files 5
Merge.taxsummary Merge tax.summary files 6
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
merger Merge two overlapping nucleic acid sequences 5
MergeSamFiles merges multiple SAM/BAM datasets into one 14
Meryl a genomic k-mer counter and sequence utility Genome assembly 6
Metabolights downloader Import public and private MetaboLights studies 2
Metabolites Correlation Analysis to highlight ion correlations considering PC-groups 1
Metagenome Contributions of OTUs to user-specified functions 2
metagenomeSeq Normalization Cumulative sum scaling 1
metaMS.runGC GC-MS data preprocessing using metaMS package 6
MetaPhlAn2 to profile the composition of microbial communities 2
metaplasmidSPAdes extract and assembly plasmids from metagenomic data 4
metaSPAdes assembler for metagenomics datasets 9
Metastats generate principle components plot data 5
metaviralSPAdes extract and assembly viral genomes from metagenomic data 4
MetFrag in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra 3
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 5
MINE - Maximal Information-based Nonparametric Exploration 2
Mismatch Profile calculates the distribution of mismatches across reads 3
mixmodel ANOVA for repeated measures statistics 1
Model temporal trend with a simple linear regression 1
Model Validation includes cross_validate, cross_val_predict, learning_curve, and more 11
MOL2 to MOL 3
msbar Mutate sequence beyond all recognition 5
msconvert Convert and filter a mass spec peak list 5
msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report 1
MSnbase readMSData Imports mass-spectrometry data files 3
msPurity.averageFragSpectra Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All) 6
msPurity.combineAnnotations Combine, score and rank metabolite annotation results 6
msPurity.createDatabase Create and SQLite database of an LC-MS(/MS) experiment 6
msPurity.createMSP Create MSP files from msPurity processed data 6
msPurity.dimsPredictPuritySingle Calculate the anticipated precursor ion purity from a DIMS dataset. 6
msPurity.filterFragSpectra Filter fragmentations spectra associated with an XCMS feature 6
msPurity.flagRemove Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds (e.g. RSD of intensity and retention time). 6
msPurity.frag4feature Assign fragmentation spectra to XCMS features using msPurity 6
msPurity.purityA Assess acquired precursor ion purity of MS/MS spectra 6
msPurity.purityX Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset. 6
msPurity.spectralMatching Perform spectral matching to MS/MS spectral libraries 6
Multi-Join (combine multiple files) 9
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 18
multiBigwigSummary calculates average scores for a list of two or more bigwig files 18
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 17
Multivariate PCA, PLS and OPLS 2
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 5
Nanopolish eventalign - Align nanopore events to reference k-mers 3
Nanopolish methylation - Classify nucleotides as methylated or not. 3
Nanopolish polyA - Estimate the length of the poly-A tail on direct RNA reads. 3
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 3
NanopolishComp: EventalignCollapse by kmers rather than by event 2
NanopolishComp: FreqMethCalculate calculates methylation frequency at genomic CpG sites 1
NCBI Accession Download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 16
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 13
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 16
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 14
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 17
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 12
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 13
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 18
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
Nearest Neighbors Classification 11
needle Needleman-Wunsch global alignment 5
NetCDF xarray Coordinate Info Get values for each coordinate of a Netcdf file 3
NetCDF xarray map plotting Visualize netCDF variables on a geographical map 2
NetCDF xarray Metadata Info summarize content of a Netcdf file 4
NetCDF xarray operations manipulate xarray from netCDF and save back to netCDF 2
NetCDF xarray Selection extracts variable values with custom conditions on dimensions 4
newcpgreport Report CpG rich areas 5
newcpgseek Reports CpG rich region 5
Newick Display visualize a phylogenetic tree Phylogenetic tree visualisation 2
newseq Type in a short new sequence 5
NextAlign Viral genome sequence alignment 13
Nextclade Viral genome clade assignment, mutation calling, and sequence quality checks 16
NGSfilter Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers 3
Nmds generate non-metric multidimensional scaling data 6
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 2
NMR_Annotation Annotation of complex mixture NMR spectra and metabolite proportion estimation 1
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 4
NMR_Preprocessing Preprocessing of 1D NMR spectra 4
NMR_Read Read Bruker NMR raw files 3
noreturn Removes carriage return from ASCII files 5
Normalization Normalization of (preprocessed) spectra 4
Normalize the relative abundance of each OTU by the predicted number of 16S copies 2
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 14
notseq Exclude a set of sequences and write out the remaining ones 5
NOVOplasty de novo assembler for short circular genomes 3
nthseq Writes one sequence from a multiple set of sequences 5
NucBed profile the nucleotide content of intervals in a FASTA file 21
Numeric Clustering 1
Numeric Clustering 12
obiannotate Adds/Edits sequence record annotations 3
obiclean tags a set of sequences for PCR/sequencing errors identification 3
obiconvert converts sequence files to different output formats 3
obigrep Filters sequence file 3
obisort sorts sequence records according to the value of a given attribute 3
obistat computes basic statistics for attribute values 3
obitab converts sequence file to a tabular file that can be open by a spreadsheet program or R 3
obiuniq 3
octanol Displays protein hydropathy 5
oddcomp Find protein sequence regions with a biased composition 5
OGR Informations lists information about an OGR supported data source 2
OGR2ogr converts simple features data between file formats 2
OpenBabel converter for molecular formats 1
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
palindrome Looks for inverted repeats in a nucleotide sequence 5
Pangolin Phylogenetic Assignment of Outbreak Lineages 15
Parse.list Generate a List file for each group 5
Parsimony Describes whether two or more communities have the same structure 5
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 12
Paste two files side by side 1
pasteseq Insert one sequence into another 5
Pathview for pathway based data integration and visualization 1
patmatdb Search a protein sequence with a motif 5
Pca Principal Coordinate Analysis for a shared file 6
PCA plot w ggplot2 4
Pcoa Principal Coordinate Analysis for a distance matrix 5
Pcr.seqs Trim sequences 6
pepcoil Predicts coiled coil regions 5
pepinfo Plots simple amino acid properties in parallel 5
pepnet Displays proteins as a helical net 5
pepstats Protein statistics 5
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 19
pepwheel Shows protein sequences as helices 5
pepwindow Displays protein hydropathy 5
pepwindowall Displays protein hydropathy of a set of sequences 5
Perform alpha rarefaction (alpha_rarefaction) 2
Perform Best-subsets Regression 2
Perform jackknifed UPGMA clustering and building jackknifed PCoA plots (jackknifed_beta_diversity) 2
Perform LDA Linear Discriminant Analysis 2
Perform open-reference OTU picking (pick_open_reference_otus) 2
Perform OTU picking (pick_otus) 2
Perform taxonomy summaries and plots (summarize_taxa_through_plots) 2
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phylotype Assign sequences to OTUs based on taxonomy 5
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 4
Pick representative set of sequences (pick_rep_set) 2
Pileup-to-Interval condenses pileup format into ranges of bases 4
Pipeline Builder an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers 11
plasmidSPAdes extract and assembly plasmids from WGS data 4
Plot abundance with trend line 1
Plot heatmap of OTU table (make_otu_heatmap) 2
plotcon Plot quality of conservation of a sequence alignment 5
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 17
plotCoverage assesses the sequencing depth of BAM files 17
plotDEXSeq Visualization of the per gene DEXSeq results 4
plotEnrichment plots read/fragment coverage over sets of regions 13
plotFingerprint plots profiles of BAM files; useful for assesing ChIP signal strength 18
plotHeatmap creates a heatmap for score distributions across genomic regions 18
plotorf Plot potential open reading frames 5
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 17
plotProfile creates a profile plot for score distributions across genomic regions 17
Plotting tool for multiple series and graph types 5
polydot Displays all-against-all dotplots of a set of sequences 5
Pre.cluster Remove sequences due to pyrosequencing errors 5
Predict Metagenome based on the abundance of OTUs and a functional database 2
preg Regular expression search of a protein sequence 7
Preprocess raw feature vectors into standardized datasets 12
Preprocess files for SARTools generate design/target file and archive for SARTools inputs 4
Preprocess population data for evolution trend analyzes 2
Presence-absence and abundance Community abundance map, presence barplot and rarefaction curves 1
prettyplot Displays aligned sequences, with colouring and boxing 5
prettyseq Output sequence with translated ranges 5
Primer.design identify sequence fragments that are specific to particular OTUs 5
primersearch Searches DNA sequences for matches with primer pairs 5
Principal Component Analysis 1
PRINSEQ to process quality of sequences 5
proFIA Preprocessing of FIA-HRMS data 2
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
Protein Database Downloader 4
PSM to SAM Generate SAM files from PSMs. 1
Pycoqc 1
pyGenomeTracks plot genomic data tracks 10
QualiMap BamQC 5
Quality format converter (ASCII-Numeric) 3
Quality Metrics Metrics and graphics to check the quality of the data 2
QualityScoreDistribution chart quality score distribution 14
QuanTP Correlation between protein and transcript abundances 2
Quast Genome assembly Quality 11
Query Reactome pathway database 4
Query Tabular using sqlite sql 8
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
Read Distribution calculates how mapped reads were distributed over genome feature 9
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 7
Read GC determines GC% and read count 7
Read NVC to check the nucleotide composition bias 7
Read Quality determines Phred quality score 7
Realign reads with LoFreq viterbi 5
Rebase GFF3 features against parent features 2
Regex Find And Replace 3
Regex Replace Regular Expression replacement using the Python re module 1
Regroup a HUMAnN2 generated table by features 4
Reheader copy SAM/BAM header between datasets 4
Remove beginning of a file 1
Remove columns by heading 1
Remove sequencing artifacts 5
Remove.dists Removes distances from a phylip or column file 6
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 5
Remove.lineage Picks by taxon 5
Remove.otulabels Removes OTU labels 6
Remove.otus Removes OTUs from various file formats 5
Remove.rare Remove rare OTUs 5
Remove.seqs Remove sequences by name 6
Rename sequences 5
Rename.seqs Rename sequences by concatenating the group name 2
Renormalize a HUMAnN2 generated table 4
ReorderSam reorder reads to match ordering in reference sequences 17
RepeatMasker screen DNA sequences for interspersed repeats and low complexity regions Repeat sequence analysis 9
RepeatModeler Model repetitive DNA 1
Replace parts of text 11
Replace column by values which are defined in a convert file 2
Replace Text in a specific column 11
Replace Text in entire line 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Reverse Complement a MAF file 1
Reverse-Complement 5
Reverse.seqs Reverse complement the sequences 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
revseq Reverse and complement a sequence 5
RmDup remove PCR duplicates 5
RNA fragment size calculates the fragment size for each gene/transcript 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 17
RNA/DNA converter 5
rnaQUAST A Quality Assessment Tool for De Novo Transcriptome Assemblies 3
RNASeq samples quality check for transcript quantification 11
rnaSPAdes de novo transcriptome assembler 10
rnaviralSPAdes de novo assembler for transcriptomes, metatranscriptomes and metaviromes 4
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 10
rtsne 1
Run a core set of QIIME diversity analyses (core_diversity_analyses) 2
Run join_paired_ends on multiple files (multiple_join_paired_ends) 2
Run split_libraries_fastq on multiple files (multiple_split_libraries_fastq) 2
Sailfish transcript quantification from RNA-seq data 4
Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads 11
SAM-to-BAM convert SAM to BAM 8
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 18
Samtools fastx extract FASTA or FASTQ from alignment files 2
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools stats generate statistics for BAM dataset 6
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
SARTools DESeq2 Compare two or more biological conditions in a RNA-Seq framework with DESeq2 4
SARTools edgeR Compare two or more biological conditions in a RNA-Seq framework with edgeR 4
Scatterplot of two numeric columns 4
Scatterplot with ggplot2 6
Screen.seqs Screen sequences 6
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 22
Search in textfiles (grep) 10
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression Filtering 3
Select first lines from a dataset Filtering 3
Select first lines from a dataset (head) 8
Select last lines from a dataset 2
Select last lines from a dataset (tail) 8
Select random lines from a file 2
Sens.spec Determine the quality of OTU assignment 6
Seq.error assess error rates in sequencing data 5
seqmatchall All-against-all comparison of a set of sequences 5
seqret Reads and writes sequences 5
seqtk_comp get the nucleotide composition of FASTA/Q 6
seqtk_cutN cut sequence at long N 6
seqtk_dropse drop unpaired from interleaved Paired End FASTA/Q 6
seqtk_fqchk fastq QC (base/quality summary) 6
seqtk_hety regional heterozygosity 6
seqtk_listhet extract the position of each het 6
seqtk_mergefa merge two FASTA/Q files 6
seqtk_mergepe interleave two unpaired FASTA/Q files for a paired-end file 6
seqtk_mutfa point mutate FASTA at specified positions 6
seqtk_randbase choose a random base from hets 6
seqtk_sample random subsample of fasta or fastq sequences 6
seqtk_seq common transformation of FASTA/Q 6
seqtk_subseq extract subsequences from FASTA/Q files 6
seqtk_trimfq trim FASTQ using the Phred algorithm 6
Sequence composition Count bases or amino-acids 3
Sequence Logo generator for fasta (eg Clustal alignments) 2
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
showfeat Show features of a sequence 5
shuffleseq Shuffles a set of sequences maintaining composition 5
SICER Statistical approach for the Identification of ChIP-Enriched Regions 3
Sickle windowed adaptive trimming of FASTQ data 4
sigcleave Reports protein signal cleavage sites 5
SIRIUS-CSI:FingerID is used to identify metabolites using single and tandem mass spectrometry 7
sirna Finds siRNA duplexes in mRNA 5
sixpack Display a DNA sequence with 6-frame translation and ORFs 7
skipseq Reads and writes sequences, skipping first few 5
Slice BAM by genomic regions 5
Slice VCF to get data from selected regions 1
SMILES to MOL 3
SMILES to SMILES 3
SnpEff build: database from Genbank or GFF record 12
SnpEff chromosome-info: list chromosome names/lengths 7
SnpEff databases: list available databases 12
SnpEff download: download a pre-built database 15
SnpEff eff: annotate variants for SARS-CoV-2 1
SnpEff eff: annotate variants 13
SnpSift Annotate SNPs from dbSnp 8
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 8
SnpSift Extract Fields from a VCF file into a tabular file 6
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 8
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for VCF specification compliance 7
Sort data in ascending or descending order 3
Sort data in ascending or descending order 10
Sort a row according to their columns 11
Sort assembly 4
Sort Column Order by heading 1
Sort.seqs put sequences in different files in the same order 6
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for regular and single-cell projects Genome assembly 13
Sparse Matrix Functions for manipulating 2-D Scipy sparse numeric data 11
Spatial coordinates anonymization without loss of the spatial relationships 1
Split BAM dataset on readgroups 4
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 file to dataset collection 7
Split libraries according to barcodes specified in mapping file (split_libraries) 2
Split MAF blocks by Species 1
Split.abund Separate sequences into rare and abundant groups 5
Split.groups Generates a fasta file for each group 5
splitter Split a sequence into (overlapping) smaller sequences 5
Stacks2: clone filter Identify PCR clones 5
Stacks2: cstacks Generate catalog of loci 5
Stacks2: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 5
Stacks2: gstacks Call variants, genotypes and haplotype 5
Stacks2: kmer filter Identify PCR clones 5
Stacks2: populations Calculate population-level summary statistics 5
Stacks2: process radtags the Stacks demultiplexing script 5
Stacks2: process shortreads fast cleaning of randomly sheared genomic or transcriptomic data 5
Stacks2: reference map the Stacks pipeline with a reference genome (ref_map.pl) 5
Stacks2: sstacks Match samples to the catalog 5
Stacks2: tsv2bam Sort reads by RAD locus 5
Stacks2: ustacks Identify unique stacks 5
Statistics on presence-absence of a numeric variable 1
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 14
StringTie merge transcripts 8
Sub-sample sequences files e.g. to reduce coverage 4
Sub.sample Create a sub sample 5
Subtract the intervals of two datasets Filtering 5
Subtract Whole Dataset from another dataset 2
Summarize taxa and store results in a new table or appended to an existing mapping file (summarize_taxa) 2
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 6
Summary.seqs Summarize the quality of sequences 5
Summary.shared Summary of calculator values for OTUs 5
Summary.single Summary of calculator values for OTUs 6
Summary.tax Assign sequences to taxonomy 5
supermatcher Match large sequences against one or more other sequences 5
Support vector machines (SVMs) for classification 12
syco Synonymous codon usage Gribskov statistic plot 5
T Test for Two Samples 2
Table Compute computes operations on table data 3
Table Merge Merging dataMatrix with a metadata table 2
Tabular to FASTQ converter Conversion 5
Tabular-to-FASTA converts tabular file to FASTA format 2
tac reverse a file (reverse cat) 8
Tadarida data cleaner clean data from animal detection on acoustic recordings 1
Tadarida identifications validation Integrate identifications from animal detection on acoustic recordings 1
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 2
tcode Fickett TESTCODE statistic to identify protein-coding DNA 5
Temporal trend indicator using GlmmTMB or GAM models 2
Text reformatting with awk 12
Text transformation with sed 10
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
tmap Displays membrane spanning regions 5
Train Augustus ab-initio gene predictor 5
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 5
TransDecoder finds coding regions within transcripts 7
transeq Translate nucleic acid sequences 5
Transformation Transforms the dataMatrix intensity values 1
Transpose rows/columns in a tabular file 3
Tree.shared Generate a newick tree for dissimilarity among groups 5
Trim leading or trailing characters 2
Trim Galore! Quality and adapter trimmer of reads 9
Trim sequences 5
Trim.flows partition by barcode, trim to length, cull by length and mismatches 5
Trim.seqs Trim sequences - primers, barcodes, quality 5
trimest Trim poly-A tails off EST sequences 5
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
trimseq Trim ambiguous bits off the ends of sequences 5
Trinity de novo assembly of RNA-Seq data 15
twofeat Finds neighbouring pairs of features in sequences 5
Unfold columns from a table 10
unifrac.unweighted Describes whether two or more communities have the same structure 5
unifrac.weighted Describes whether two or more communities have the same structure 5
union Reads sequence fragments and builds one sequence 5
Unique occurrences of each record 8
Unique occurrences of each record 1
Unique lines assuming sorted input file 10
Unique.seqs Return unique sequences 5
Univariate Univariate statistics 2
Upload File from your computer Query and retrieval 3
ValidateSamFile assess validity of SAM/BAM dataset 14
Variables exploration Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data 1
Variant Frequency Plot Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data Aggregation 4
VarScan for variant detection 2
VarScan copynumber Determine relative tumor copy number from tumor-normal pileups 4
VarScan mpileup for variant detection 4
VarScan somatic Call germline/somatic and LOH variants from tumor-normal sample pairs 9
VCF to MAF Custom Track for display at UCSC 2
VCF-BEDintersect: Intersect VCF and BED datasets 5
VCF-VCFintersect: Intersect two VCF datasets 5
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 5
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 5
VCFannotate: Intersect VCF records with BED annotations 5
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 5
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 5
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 6
VCFcommonSamples: Output records belonging to samples common between two datasets 5
VCFdistance: Calculate distance to the nearest variant 5
VCFfilter: filter VCF data in a variety of attributes 8
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 5
VCFgenotypes: Convert numerical representation of genotypes to allelic 5
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 5
VCFleftAlign: Left-align indels and complex variants in VCF dataset 5
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 5
VCFselectsamples: Select samples from a VCF dataset 5
VCFsort: Sort VCF dataset by coordinate 6
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 6
vectorstrip Strips out DNA between a pair of vector sequences 5
Venn Generate Venn diagrams for groups 5
Venn diagram [JVenn] 4
Venn Diagram from lists 6
Violin plot w ggplot2 5
Visualize with Krona Visualise any hierarchical data 1
Volcano Plot create a volcano plot Visualisation 5
VSearch alignment Chimera detection Sequence clustering Sequence masking 6
VSearch chimera detection Chimera detection Sequence clustering Sequence masking 6
VSearch clustering Chimera detection Sequence clustering Sequence masking 7
VSearch dereplication Chimera detection Sequence clustering Sequence masking 7
VSearch masking Chimera detection Sequence clustering Sequence masking 6
VSearch search Chimera detection Sequence clustering Sequence masking 6
VSearch shuffling Chimera detection Sequence clustering Sequence masking 6
VSearch sorting Chimera detection Sequence clustering Sequence masking 7
water Smith-Waterman local alignment 5
Wavelet variance using Discrete Wavelet Transfoms 3
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
wobble Wobble base plot 5
wordcount Counts words of a specified size in a DNA sequence 5
wordmatch Finds all exact matches of a given size between 2 sequences 5
xcms adjustRtime (retcor) Retention Time Correction 7
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 7
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 8
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 5
xcms get a sampleMetadata file which need to be filled with extra information 3
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 8
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 5
xcms process history Create a summary of XCMS analysis 8
XSeeker Preparator Prepare RData file from CAMERA to be visualized in XSeeker Formatting Parsing 7