Language,name_tool
C++,"Mascot Server"
Perl,"Mascot Server"
MATLAB,microManager
C++,microManager
Python,microManager
Perl,PolyPhen-2
Shell,bedtools_genomecoveragebed_histogram
Python,bedtools_genomecoveragebed_histogram
C++,DSSP
C++,AUGUSTUS
R,FlowSOM
C++,MACH
C++,MaCH-Admix
PHP,Orphadata
Java,dbNSFP
Python,Oncotator
Perl,GeneMatcher
Python,GeneMatcher
Perl,SPICKER
C++,Chimera
Python,Chimera
C++,AMBER
Fortran,AMBER
C,AMBER
C++,"AutoDock Vina"
Python,MDAnalysis
Java,SearchGUI
C++,Comet
MATLAB,ModPred
Python,ModPred
Java,TM-score
Perl,MUpro
Perl,ClusPro
C,SCRWL
Java,"PEAKS De Novo"
R,DEPIB
Python,DEPIB
Perl,reprof
Java,JEvTrace
C,FUGUE
Java,IMOD
Python,SPIDER
C++,LZerD
Fortran,AQUA
C,AQUA
Python,ChemProps
JavaScript,Ginkgo
R,Ginkgo
C++,Ginkgo
PHP,Ginkgo
Shell,Ginkgo
Python,"Reciprocal Smallest Distance (RSD)"
Perl,MISA
Perl,SMOOTH
Pascal,SMOOTH
Java,GEC
Python,ASNR
Python,MichelaNglo
JavaScript,MichelaNglo
PyMOL,MichelaNglo
Java,Hydrophobicity
Perl,Ktreedist
C,BAMscale
R,BAMscale
R,flowClean
Python,NL4DV
Perl,ContigExtender
Python,ContigExtender
Python,AREM
R,pksensi
Perl,RNAz
Perl,"Andrej Sali Lab"
Java,Kaks_Calculator
C++,Kaks_Calculator
R,SKAT
R,MetaSKAT
Python,InterVar
Python,MSMBuilder
Perl,PROTOMAP
R,CompositeDriver
Java,Juicebox
Shell,Juicebox
Python,MHCflurry
Python,CoroNet
R,EpiEstim
Perl,"MMTSB toolset"
C++,SerialEM
Shell,Frealign
C++,EMAN
Java,TBtools
R,UALCAN
MATLAB,LST
C++,SOLAR-eclipse
Fortran,SOLAR-eclipse
C,SOLAR-eclipse
MATLAB,Lead-DBS
C++,GS-align
C++,QuEST
Java,SAAP-BS
Perl,SAAP-BS
Python,SAAP-BS
C++,RasMol
C,RasMol
PHP,PSORT.org
JavaScript,PSORT.org
C,srnaloop
R,VEGAS2
Shell,VEGAS2
Perl,VEGAS2
C++,PeptideProphet
Perl,PeptideProphet
Perl,ProteinProphet
C,ProteinProphet
C++,ASAPRatio
C++,PepNovo
Python,InsPecT
Java,mzMatch
R,CAMERA
C++,OMSSA
C++,MyriMatch
Python,PsRRR
R,MSCquartets
Java,"Pseudomonas Genome Database"
Perl,"Pseudomonas Genome Database"
Python,Cox-PASNet
Java,Quant
C,Quant
Python,tax2tree
Python,dRep
C++,vcf2diploid
R,ActiveDriver
MATLAB,"Visualisation tools"
Javascript,SNPTEST
C++,SNPTEST
JavaScript,SNPTEST
Java,SeqMonk
R,Enterotyping
C,PSMC
PHP,"Banana Genome Hub"
JavaScript,"Banana Genome Hub"
MATLAB,MutSig2CV
C++,DNENRICH
R,SPP
Perl,PeakSeq
C,PeakSeq
C++,Cufflinks
C,Cufflinks
Java,Scripture
Java,IGV
Java,Trinity
C++,Trinity
C++,ProteoWizard
Python,PICRUSt
R,LACHESIS
C++,LACHESIS
C++,OpenSWATH
C++,Sailfish
C,Sailfish
R,scLVM
Python,scLVM
Java,Peptide-shaker
C++,StringTie
C,StringTie
R,ballgown
R,COMPASS
Python,kallisto
Python,EVmutation
Groovy,Nextflow
C++,demuxlet
Python,FORECasT
C++,XPRESS
PHP,ENDEAVOUR
Java,ENDEAVOUR
Java,APEX
Perl,MiRDeep
R,Batman
R,MDscan
Perl,MDscan
Python,RODEO
C++,Kaiju
Java,MS-GF+
C,Cortex
C++,GEMMA
Python,MSMC
D,MSMC
Shell,platypus
R,"Genome STRiP"
Java,"Genome STRiP"
Python,LDSC
R,DANPOS
Python,DANPOS
R,RTNduals
R,viper
C++,Minimac3
C,Minimac3
Python,CESAM
C++,Graphtyper
C,MrCaNaVaR
C++,EMMAX
C,EMMAX
R,Syzygy
Python,Syzygy
PHP,"Cocoa Genome Hub"
JavaScript,"Cocoa Genome Hub"
R,GenePattern
Java,GenePattern
Perl,GenePattern
Java,FLOSS
Python,"Mosaic Vaccine Designer"
Python,ERANGE
MATLAB,SegSeq
Perl,Phymm
Perl,PyroNoise
C++,BreakDancer
Perl,BreakDancer
Perl,ALEXA-Seq
Python,Trans-ABySS
Python,MISO
C,MISO
C,SAINT
Python,FaST-LMM
C++,HH-suite
C,HH-suite
Java,ChromHMM
C++,"Bowtie 2"
Python,Segway
Python,MetaPhlAn
Java,"ImageJ (NIH)"
Python,SpecI
R,metagenomeSeq
Perl,"Metagenomic operational taxonomic units (mOTUs)"
R,scde
R,RnBeads
Shell,Diamond
R,ABarray
Java,DIA-Umpire
Python,HISAT2
Java,MiXCR
Python,SVTyper
R,Oscope
R,RiboTaper
R,dada2
R,IHW
Python,TRIC
C++,CRAC
R,monocle
C++,nanopolish
Python,signalAlign
C++,Salmon
Python,umis
R,SC3
R,SCnorm
Python,CIRCLE-seq
R,sleuth
R,chromVAR
R,"Monocle 2"
C++,MECAT
C,MECAT
R,AUCell
R,scmap
Perl,POLYPHEN
R,SHOREmap
Perl,SHOREmap
Java,iceLogo
R,matchBox
Perl,decoy.pl
Fortran,CNSsolve
C,CNSsolve
R,biomaRt
Java,RaptorX
R,EasyQC
Java,CoNet
Perl,SymCurv
R,zinbwave
R,MetaNeighbor
PHP,"Sugarcane Genome Hub"
JavaScript,"Sugarcane Genome Hub"
Python,DCA
Python,inDelphi
Python,HMP2
C++,Flye
Python,Flye
C,Flye
Python,QIIME2.0
Python,PICRUSt2
C++,NGMLR
R,Bioconda
Java,Bioconda
C++,Bioconda
Fortran,Bioconda
C,Bioconda
Python,scScope
Python,Py-EM
Python,Prosit
R,Garnett
C++,Warp
C#,Warp
C,Warp
Python,ilastik
C,ilastik
R,Harmony-R
Shell,Harmony-R
C++,Harmony-R
C,wtdbg2
MATLAB,"COBRA Toolbox"
R,MicrobiomeAnalyst
Python,PhageTerm
R,CMScaller
Java,QuPath
PHP,SwissADME
JavaScript,SwissADME
R,ReactomePA
Java,TCS
R,Gene-PROBER
Java,OpenCASA
C++,ParDRe
Python,multiplierz
Python,pymbar
R,MotifRegressor
Perl,MotifRegressor
Java,JSpecies
C++,Allpaths-LG
Python,2020plus
R,consensusDE
R,NetGSA
C++,NetGSA
Shell,BioNetFit
Perl,BioNetFit
Python,DeepRKE
R,gprege
R,"La isla de tomato"
Java,Luciphor2
C#,CEQer
Pascal,LINKAGE
R,PHI-Nets
Java,PHI-Nets
Java,Multi-Harmony
Python,"Reciprocal Best Hits - Best Bidirectional Hits"
Java,"PEAKS DB"
R,Mayu
Perl,Mayu
C++,INFO-RNA
Python,DATMA
Shell,DATMA
C++,Pedcheck
C,Pedcheck
C++,QTDT
C++,PHASE
Perl,infocalc
R,SNPSpD
Perl,ANCESTRYMAP
C,ANCESTRYMAP
R,SABER
Java,SABER
Java,GMDR
Perl,GMDR
C++,PLINK
C,PLINK
Java,BEAGLE
MATLAB,RADIOMICS
Java,GINsim
C++,Ray
Python,HotNet
Perl,Opera
C++,IsoLasso
Python,SPAdes
R,clusterProfiler
R,"Pathway Tools"
Java,"Pathway Tools"
Perl,"Pathway Tools"
Java,IGVtools
Python,MAFFT
R,PAML
Fortran,"ESPript 3.0"
Java,VISTA
C,Lucy
Perl,MotifSampler
C,MrBayes
Perl,Twinscan
C,ms
C,TREE-PUZZLE
R,vsn
R,RMAExpress
Java,SBML
R,SBML
Ruby,SBML
C#,SBML
Python,SBML
C++,SBML
R,R-QTL
R,affycomp
C++,XTandem
C++,Glimmer-HMM
C,Glimmer-HMM
Java,"Java Treeview"
Java,HaploView
C++,PILER
Python,PILER
C++,SGA
R,safe
Shell,GMAP
C,GMAP
Python,PMut
C,RONN
R,simpleaffy
R,aCGH
R,RLMM
R,affylmGUI
R,topGO
R,RankProd
C++,COPASI
JavaScript,"Interactive Tree Of Life (iTOL)"
R,GOstats
Python,ARIA
Perl,SSAKE
Java,Gepard
Perl,CEGMA
R,GEOquery
"Visual Basic","VIPER LC-MS"
Java,TASSEL
R,beadarray
Perl,VCAKE
C,VCAKE
C++,SOAP
C++,LibSBML
C,LibSBML
R,DAnTE
Java,Ontologizer
Java,"FindPeaks 4.0 (Vancouver Short Read Package)"
R,mzR
C++,mzR
C++,SeqMap
Java,F-seq
Perl,CABOG
R,SPIA
Java,DNAPlotter
R,CleaveLand4
Perl,CleaveLand4
R,arrayQuality
SQL,"IslandViewer 4"
C++,QMSIM
C++,TopHat
Python,Biopython
Java,CloudBurst
C,BWA
R,rtracklayer
Python,SICER
C++,trimAl
Java,VarScan
C++,Pindel
Perl,"SNP ratio test"
Java,IGB
R,DEGseq
Java,Tablet
C++,RSEM
C++,BEDTools
C,SNVMix
C#,Skyline
Perl,GSNAP
C,GSNAP
R,GOSemSim
Perl,PheWAS
R,ConsensusClusterPlus
Python,DendroPy
Perl,PSORTb
C++,Metal
C,bedGraphToBigWig
JavaScript,"Cytoscape Web"
R,oligo
Java,GeneMANIA
Perl,SSPACE
Ruby,Jellyfish
C++,Jellyfish
Perl,Jellyfish
Python,Jellyfish
Perl,PRINSEQ
Python,BeatsonLab-MicrobialGenomics
Perl,Bismark
Python,ProDy
C++,BamTools
Java,SequenceVariantAnalyzer
C++,VCFtools
Perl,VCFtools
Perl,RUM
Python,RUM
Java,ContEst
R,ExomeCNV
Python,ChimeraScan
Java,Seal
C,FLASH
Python,Pybedtools
R,PoPoolation2
Perl,PoPoolation2
Java,Artemis
C++,ART
Perl,ART
Shell,ART
C++,"Multi Experiment Matrix"
Perl,"Multi Experiment Matrix"
Python,"Multi Experiment Matrix"
R,Rehh
R,Contra
Python,Contra
R,GEM
Java,RNA-SeQC
Java,Geneious
R,BitSeq
Perl,Strelka
C++,Bedops
Java,"ADAPTER REMOVAL"
R,GUniFrac
Python,Delly2
R,GAPIT
Python,Snakemake
R,QualiMap
Java,QualiMap
R,HiCNorm
R,SNPRelate
C++,SortMeRna
C++,STAR
Java,Bedutils
R,RepeatExplorer
Perl,RepeatExplorer
Python,RepeatExplorer
Perl,QUAST
Python,QUAST
C,QUAST
R,EBSeq
R,TANGO
R,pathview
R,KmerGenie
C++,KmerGenie
Python,KmerGenie
Python,OncodriveCLUST
C++,NextGenMap
C++,PEAR
R,MEDIPS
R,FeatureCounts
C,NextClip
C++,MSIsensor
R,ngsTools
R,bumphunter
Python,PyRAD
Python,pRESTO
Java,ThunderSTORM
R,MSstats
C++,MIPgen
R,circlize
Python,STAMP
C,SVDquartets
C++,LoRDEC
Python,Poretools
Python,HTSeq
R,DOSE
C++,"minimac 2"
C,MetaPSICOV
R,PRSice
R,MethylMix
C++,MEGAHIT
Ruby,PolyMarker
MATLAB,SNN-Cliq
Python,SNN-Cliq
D,Sambamba
C,vt
R,ChIPseeker
Java,MeDuSa
Python,MeDuSa
Java,HAlign
C,ExaML
Java,ASTRAL
C++,AncesTree
Python,AncesTree
R,polyester
R,Tax4Fun
R,GOplot
R,Mango
C++,Mango
Python,BUSCO
R,SomaticSignatures
Perl,Roary
R,missMethyl
R,LOLA
Java,tcsBU
C++,MaxBin
Perl,MaxBin
Python,PHYLUCE
Perl,BRAKER1
R,genefu
Python,MetaQUAST
C++,Manta
Python,Manta
R,destiny
R,ComplexHeatmap
Python,MultiQC
R,Assemblytics
Perl,Assemblytics
Python,Assemblytics
Java,MorphoLibJ
JavaScript,Cas-analyzer
Python,KAT
C++,KAT
R,minfi
R,scater
C,mPTP
R,synergyfinder
Java,"Trainable Weka Segmentation"
R,karyoploteR
R,UpSetR
Python,UpSetR
Python,DFAST
R,FROGS
Perl,FROGS
Python,FROGS
Python,NanoPack
Javascript,Minimap2
Python,Minimap2
C,Minimap2
JavaScript,Minimap2
R,IRscope
Perl,PopLDdecay
Python,GTDB-Tk
R,TCC
R,"Conditional quantile normalization"
C++,SOAPnuke
R,MendelianRandomization
C,FastTree
Java,BEAST
R,LFMM
C,LFMM
R,selscan
Shell,selscan
C++,selscan
C++,SLiM
C++,ModelTest-NG
R,"R functions for cDNA array analysis"
Java,"Database of interacting proteins (DIP)"
Java,Ensembl
SQL,Ensembl
Perl,Ensembl
C,Ensembl
R,genomation
Java,"Ribosomal Database Project (RDP)"
SQL,"Stanford Microarray Database (SMD)"
Java,MIAMExpress
Python,ExPASy
C,"Vienna RNA Package"
Python,JASPAR
Shell,ARB
C++,ARB
Perl,ARB
Python,PDB2PQR
C++,FATCAT
Perl,FATCAT
Perl,miRU
C++,FoldX
PHP,WebGestalt
Java,"The GRID"
Perl,WEGO
PHP,"QGRS Mapper"
Java,"QGRS Mapper"
Perl,PAL2NAL
Perl,"LIPID MAPS"
Java,HMDB
Perl,HMDB
MATLAB,QuantiSNP
PHP,STAMP
C++,STAMP
Perl,STAMP
Perl,Primer3Plus
C,Primer3Plus
Java,CPC
Java,PPS
Perl,"Jpred 3"
Java,CS23D
C++,CS23D
Perl,CS23D
Python,CS23D
C,CS23D
Java,"IMGT V-QUEST"
Perl,SISSRs
JavaScript,"Human Splicing Finder"
Java,MiRanalyzer
Perl,MiRanalyzer
Ruby,GeneCodis3
C++,GeneCodis3
Java,"ToppGene Suite"
Python,eggNOG
R,Solas
Perl,CATH
Perl,Reactome
C++,SRA
Perl,SRA
C,SRA
SQL,miRBase
SQL,starBase
SQL,lncRNAdb
Perl,RATT
R,QuasR
PHP,agriGO
Java,Dali
Java,3DLigandSite
Ruby,GUIDANCE
Perl,GUIDANCE
C,GUIDANCE
C,SMOG
Perl,ANNOVAR
C++,MapSplice
Python,MapSplice
Perl,ShoRAH
Python,ShoRAH
Perl,FragGeneScan
C,FragGeneScan
Java,IKMC
Python,IKMC
PHP,TADB
JavaScript,TADB
Perl,TADB
PHP,CLIPZ
Java,CLIPZ
Java,YEASTRACT
SQL,NONCODE
PHP,R.E.D.
Java,R.E.D.
PHP,SwissDock
Perl,SwissDock
Python,SwissDock
Perl,HMMER3
C,HMMER3
Python,antiSMASH
Java,SNVer
Python,ExoCarta
PHP,Phytozome
Java,Phytozome
SQL,Phytozome
Perl,Phytozome
Java,DO
Java,VFDB
R,cn.mops
R,edgeR
R,QuaternaryProd
Perl,dbCAN
Python,METAGENassist
Java,SIFT
Perl,SIFT
R,RobiNA
Java,RobiNA
Java,"The Flux Capacitor"
R,OncodriveFM
Perl,OncodriveFM
Python,miRmap
R,Rsubread
Java,"Apache Taverna"
Ruby,"Apache Taverna"
Java,"EBI Tools"
Perl,"EBI Tools"
R,ComiR
Java,aLeaves
Shell,GalaxyRefine
C,Gubbins
Python,Gubbins
Python,DeepTools
R,CHOPCHOP
JavaScript,CFM-ID
Ruby,CFM-ID
SQL,CFM-ID
Java,"LINCS Canvas Browser (LCB)"
C++,LeeHom
R,limma
JavaScript,WikiPathways
SQL,GPCRDB
Python,GPCRDB
R,TCGAbiolinks
Python,PLIP
C++,PHMMER
JavaScript,DIANA-mirPath
PHP,DIANA-mirPath
SQL,DIANA-mirPath
R,ClustVis
Java,TOPCONS
JavaScript,OrthoVenn
R,NOISeq
Perl,SRAMP
Javascript,PHASTER
JavaScript,PHASTER
R,TSCAN
R,FACETS
Perl,FACETS
Java,REDIportal
SQL,REDIportal
Python,REDIportal
Java,stringApp
Python,ExAC
JavaScript,Rfam
Python,Rfam
R,rWikiPathways
PHP,PharmMapper
Python,PharmMapper
R,NOREVA
PHP,RMBase
JavaScript,RMBase
Python,DynaMut
R,"MetaboAnalyst 4.0"
Java,"MetaboAnalyst 4.0"
JavaScript,WEGO2.0
Java,WEGO2.0
Ruby,MiGA
Java,GENCODE
Perl,GENCODE
Python,GENCODE
Ruby,GENCODE
Python,AnnoTree
Perl,SGI
C++,BEAGLE
Java,Dendroscope3
Shell,"AGS ACN"
Java,"FACTA plus"
Java,OAT
C,Velvet
C++,MAQ
Perl,MAQ
R,MEDME
C++,GERMLINE
C++,SOAPsnp
C,SOAPsnp
C,VariationHunter
C++,ABySS
Perl,Circos
R,RDXplorer
Python,RDXplorer
JavaScript,JBrowse
Perl,JBrowse
C++,SOAPdenovo
C,SOAPdenovo
C,Geneid
C++,GLASS
Java,GATK
Python,GATK
Python,Stampy
Python,Dindel
Perl,ChimeraSlayer
C++,CNVnator
Java,MEGAN6
R,MuSiC2
Perl,MuSiC2
Python,MuSiC2
R,LobSTR
C++,LobSTR
Python,LobSTR
R,FitHiC
Python,"The Human Protein Reference Database (HPRD)"
R,TitanCNA
R,GOTHiC
Python,CheckM
Perl,Wise2.4
C++,MIRA
C,Multiz
Python,HiRise
Shell,HiRise
Shell,UMI-tools
Python,UMI-tools
C++,Centrifuge
Shell,CANU
Perl,CANU
R,hicrep
Java,Mauve
C++,Mauve
C,BLAT
Java,MAPP
Shell,SweeD
C++,SweeD
C,SweeD
Perl,SHARCGS
Python,PyroMap
Python,MiRScan
C++,PennCNV
Perl,PennCNV
C,Phred
C,"Phred Phrap Consed Cross match"
Python,buccaneer
Python,BALBES
Python,PHENIX
Fortran,Refmac
Java,PXImage
MATLAB,"mRMR Feature Selection"
Perl,CLUMPAK
Perl,Metaxa2
R,pophelper
C,GControl
Perl,SLP
Python,msatcommander
R,Arlequin
C++,Stacks
MATLAB,Oufti
R,GemTools
Python,PLATA
R,GLOBETROTTER
Java,DRAWID
Python,"DExSI: Targeted GC-MS Metabolomics"
R,NGSCheckMate
Python,NGSCheckMate
Perl,3d-dna
AWK,3d-dna
C,Macrel
Python,Macrel
Shell,Macrel
R,Macrel
SQL,PhosPhAt
R,Gplas
Bash,Gplas
Python,MACARON
Java,Sequedex
Python,Sequedex
R,TANRIC
Java,TANRIC
Python,TANRIC
Shell,HTR
C++,HTR
C++,UNPHASED
R,SAM
R,gage
C++,BSMAP
R,CNV-seq
Perl,CNV-seq
C#,DeconTools
Python,"BS Seeker"
R,"Repeat Explorer"
Perl,"Repeat Explorer"
Python,"Repeat Explorer"
R,PeakAnalyzer
Java,PeakAnalyzer
C++,PeakAnalyzer
R,baySeq
R,SolexaQA
Perl,SolexaQA
C++,MAPSCI
C++,ShoRAH
R,Mulcom
Javascript,Krona
Perl,Krona
JavaScript,Krona
Shell,Blasr
C++,Blasr
Perl,Blasr
Python,Blasr
C,PANDAseq
Ruby,"Atlas Suite"
C,"Atlas Suite"
R,EpiDISH
Javascript,Enrichr
JavaScript,Enrichr
C,MIMO
Python,AUREA
C++,Skewer
Python,PLEK
C,PLEK
C,SNAP
C,Exonerate
Java,COLOMBO
Java,ARACNE
C++,ARACNE
MATLAB,"GTOM - Generalized Topological Overlaping Measure"
Java,NNN
Java,MetaQTL
JavaScript,MG-RAST
Perl,MG-RAST
Python,MG-RAST
C,MG-RAST
R,minet
C++,minet
Java,USeq
R,WGCNA
Java,BMGE
Java,"BLAST Ring Image Generator"
Perl,MetaPhyler
R,methylumi
R,IUTA
Java,BepiPred
R,GeneGA
Python,COBRApy
SQL,PrognoScan
Python,ACPYPE
R,DMRcate
Java,"Open Babel"
Python,"Open Babel"
Python,Avogadro
C,SOAPdenovo2
Java,Curtain
R,ALDEx2
MATLAB,"Reference Gene Selection"
R,Bioconductor
Python,MACS
Perl,Crossbow
Perl,PEMer
Python,PEMer
C++,Bowtie
Perl,Binning
R,DESeq
R,GOseq
Python,"The Genomic HyperBrowser"
Python,TopHat-Fusion
Java,PARalyzer
Python,Cistrome
R,bsseq
R,methylKit
R,MAnorm
MATLAB,MAnorm
Javascript,WebApollo
Java,WebApollo
Perl,WebApollo
JavaScript,WebApollo
C++,Kraken
Perl,Kraken
C++,ANGSD
R,IPO
JavaScript,InteractiVenn
R,pcaReduce
R,DrImpute
Perl,"Purge Haplotigs"
R,iDEP
Javascript,bModelTest
JavaScript,bModelTest
Java,Metagenome-Kin
R,km2gcn
R,ARRmNormalization
R,DESeq2
C++,Bridger
Perl,Bridger
Java,LICHeE
Python,OrthoFinder
R,WU-CRISPR
R,HiC-Pro
Python,HiC-Pro
Python,MAGeCK
R,MAST
R,cellity
R,deconstructSigs
Shell,EAGER
Java,EAGER
Python,EAGER
C++,SCITE
Python,"CEL-Seq 2"
Python,TanglabCircularRNAPipeline
R,CHiCAG
C++,Mash
R,GiniClust
Python,GiniClust
R,SCZEWAS
R,scDD
Python,Scoary
R,splatter
Python,SCANPY
Perl,RaGOO
Python,RaGOO
R,sctransform
C++,sctransform
Python,"Cancer Genome Interpreter (CGI)"
JavaScript,"Cancer Genome Interpreter (CGI)"
SQL,MetFrag
C++,Rcorrector
Perl,Rcorrector
C,Rcorrector
Shell,MetaWRAP
Python,MetaWRAP
R,"CyTOF workflow"
Java,ReactomeFIViz
C++,khmer
Python,khmer
Perl,HiCUP
R,tximport
Java,"CoNet app"
R,scran
MATLAB,Caserel
Delphi,PeakFinder
R,iHS
Perl,iHS
Python,enrichment
C++,LocARNA
MATLAB,N-score
R,Metastats
C,SHRiMP
C++,GERP++
C++,DeFuse
Java,CAVER
R,GenomicAlignments
Python,GEMINI
Java,PredictSNP
JavaScript,PredictSNP
Python,PredictSNP
R,Clomial
C++,ClonalFrameML
R,BASiCS
Python,msprime
Python,CNVkit
Java,Unicycler
C++,Unicycler
Python,Unicycler
C++,OpenMM
Python,OpenMM
C,OpenMM
Python,TADbit
R,mixomics
Perl,MUMmer
R,sva
C++,MSTMap
Perl,GAST
Perl,IMPUTE2
C++,ChromoPainter
C++,TreeMix
Shell,eQtlBma
R,eQtlBma
Java,MetaSim
Perl,RADtools
Java,NetBox
Python,NetBox
R,GENIE3
MATLAB,GENIE3
Python,GENIE3
Java,"Enrichment Map Cytoscape Plugin"
R,PoPoolation
Perl,PoPoolation
C++,REPET
Python,REPET
Perl,DeconSeq
C,DeconSeq
R,DirichletMultinomial
R,MultiPhen
Perl,A5
Shell,PROVEAN
R,phyloseq
Java,SNP2HLA
Perl,diffReps
R,SARTools
Java,EffectiveT3
C++,STADEN
Fortran,STADEN
C,STADEN
R,SIAMCAT
R,DOQTL
Perl,MIGRATE
C,bcftools_view
R,AdmixTools
C++,AdmixTools
Perl,AdmixTools
C,AdmixTools
Python,fastSTRUCTURE
Python,Pse-Analysis
Java,SnpSift
Python,"Diffusion Imaging in Python (DIPY)"
C++,Flexbar
Python,4mCpred-EL
R,Mfuzz
R,EPISFA
C++,cisTEM
Python,DeepPoseKit
Python,GraPhlAn
C++,Swarm
Python,AMAS
Perl,Phylosift
C++,VSEARCH
Python,scikit-image
Shell,D-GENIES
Python,D-GENIES
Python,GroopM