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Resource Name Sort Ascending Sort Descending	Proper Citation Sort Ascending Sort Descending	Abbreviations Sort Ascending Sort Descending	Resource Type Sort Ascending Sort Descending	Description	Keywords Sort Ascending Sort Descending	Resource Relationships Sort Ascending Sort Descending	Funding Sort Ascending Sort Descending	Defining Citation Sort Ascending Sort Descending	Availability	Alternate IDs	Alternate URLs	Old URLs	Resource ID	Synonyms Sort Ascending Sort Descending	Record Last Update Sort Ascending Sort Descending	Mentions Count Sort Ascending Sort Descending
Happy Resource Report Resource Website 10+ mentions	Happy (RRID:SCR_001395)	HAPPY	data analysis software, data processing software, software application, software resource, source code	THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).	qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping	is listed by: Genetic Analysis Software is listed by: Debian has parent organization: Wellcome Trust Centre for Human Genetics	Wellcome Trust	PMID:11050180 DOI:10.1073/pnas.230304397	THIS RESOURCE IS NO LONGER IN SERVICE	nlx_152594	http://www.well.ox.ac.uk/~rmott/happy.html	https://sources.debian.org/src/r-other-mott-happy.hbrem/	SCR_001395	reconstructing HAPlotYpes	2026-09-12 12:55:25	46
Wellcome Trust Centre for Human Genetics Resource Report Resource Website 10+ mentions	Wellcome Trust Centre for Human Genetics (RRID:SCR_003307)	WTCHG	data or information resource, portal, topical portal	An international leader in genetics, genomics and structural biology, and research institute of the Nuffield Department of Medicine at the University of Oxford, whose objective is to extend our understanding on how genetic inheritance makes us who we are in order to gain a clearer insight into mechanisms of health and disease. Looking across all three billion letters of the human genetic code, they aim to pinpoint variant spellings and discover how they increase or decrease an individual's risk of falling ill. They collaborate with research teams across the world on a number of large-scale studies in these areas.	genetics, genomics, structural biology	has parent organization: University of Oxford; Oxford; United Kingdom is parent organization of: Happy is parent organization of: Wellcome-CTC Mouse Strain SNP Genotype Set is parent organization of: CHAoS is parent organization of: Platypus is parent organization of: Stampy is parent organization of: GWAMA is parent organization of: cortex var	University of Oxford; Oxford; United Kingdom ; Wellcome Trust ; other sponsors		Free, Freely available	nif-0000-31897			SCR_003307		2026-09-12 12:55:55	49
Debian Resource Report Resource Website 50+ mentions	Debian (RRID:SCR_006638)	Debian	data or information resource, database, software repository, software resource, source code	Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.	operating system, software package, FASEB list	lists: GUARDD lists: FACS lists: SNAVI lists: Fusion Analyser lists: GEOquery lists: MIMOSA lists: RNAcontext lists: AffyRNADegradation lists: Patchwork lists: GraBCas lists: GENIE3 lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: Megraft lists: PeptideProphet lists: VARiD lists: Flicker lists: ARACHNE lists: Quant lists: riboPicker lists: cn.FARMS lists: ProteinProphet lists: dbSTS lists: flowPeaks lists: SODOCK lists: PEPPER lists: POPBAM lists: Micro-Analyzer lists: MuTect lists: Mfuzz lists: PGS lists: TAPyR lists: ContEst lists: FPSAC lists: FlipFlop lists: SRMA lists: Pindel lists: PhenoFam lists: DSRC lists: SOAP lists: TriageTools lists: StringTie lists: SplitSeek lists: BLASR lists: Bowtie lists: Barrnap lists: MUSCLE lists: GimmeMotifs lists: massiR lists: CUDA-EC lists: Illuminator lists: SplicePlot lists: SLOPE lists: PARalyzer lists: VAAL lists: BreakSeq lists: ProGlycProt lists: OmicsOffice for NGS SeqSolve lists: TileQC lists: NGSUtils lists: QUAST lists: GenomicTools lists: piCALL lists: SNPchip lists: TALLYMER lists: SABER lists: wateRmelon lists: QualiMap lists: BFCounter lists: ADMIXTURE lists: OLIN lists: DEXUS lists: limmaGUI lists: KAnalyze lists: oneChannelGUI lists: BeadDataPackR lists: affylmGUI lists: SAMBLASTER lists: PyLOH lists: fRMA lists: CYCLE lists: FARMS lists: MACAT lists: GlyProt lists: YinOYang lists: Sequedex lists: DictyOGlyc lists: ToppCluster lists: Biocatalogue - The Life Science Web Services Registry lists: ProbRNA lists: HAPLOPAINTER lists: Chilibot: Gene and Protein relationships from MEDLINE lists: GERMLINE lists: FACTA+. lists: CisGenome lists: asSeq lists: unifiedWMWqPCR lists: HOMOZYGOSITYMAPPER lists: Prediction of Amyloid Structure Aggregation lists: InterMine lists: TANGO lists: CQN lists: MEME Suite - Motif-based sequence analysis tools lists: pRESTO lists: S-MART lists: PhosphoSitePlus: Protein Modification Site lists: myExperiment lists: DINDEL lists: Skylign lists: PEDIGRAPH lists: ADaCGH2 lists: CCAT lists: AnimalTFDB lists: TEMP lists: CanSNPer lists: Candida Genome Database lists: SamSPECTRAL lists: InteroPorc lists: MetaBase lists: Pecan lists: cisRED: cis-regulatory element lists: AffyPipe lists: SHORTY lists: BISC lists: Pathway Commons lists: Cake lists: SNVer lists: WebGeSTer DB lists: FlyFactorSurvey lists: ASPGD lists: TcoF lists: cpnDB: A Chaperonin Database lists: ZOOM lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: BEETL-fastq lists: NGSrich lists: ShotGun lists: Iterative Signature Algorithm lists: SBARS lists: SNPAAMapper lists: Autophagy Database lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: EchoBASE lists: QualitySNPng lists: Pathview lists: pymzML lists: RopeBWT2 lists: ExomeDepth lists: NetPathMiner lists: leeHom lists: PurBayes lists: libCSAM lists: SuperPred: Drug classification and target prediction lists: HGNC lists: Coding Potential Calculator lists: T3DB lists: CPTRA lists: BioNumbers lists: GATE lists: ProRata lists: GreenPhylDB lists: BREAKDANCER lists: GeneFisher lists: tweeDEseq lists: HYDEN lists: Eukaryotic Linear Motif lists: Primer3Plus lists: MethylAid lists: Triplex lists: Distant Regulatory Elements lists: hot scan lists: MFEprimer lists: Proteome Analyst Specialized Subcellular Localization Server lists: mrsFAST lists: BioJS lists: FastSNP lists: Gene Set Enrichment Analysis lists: Pipeliner lists: ms lims lists: GenePattern lists: rBiopaxParser lists: QDNAseq lists: MutDB lists: Piano lists: NovelSeq lists: MAGE-TAB lists: Database of Interacting Proteins (DIP) lists: Weighted Gene Co-expression Network Analysis lists: Blood Group Antigen Gene Mutation Database lists: drFAST lists: pairheatmap lists: MiST - Microbial Signal Transduction database lists: AltAnalyze - Alternative Splicing Analysis Tool lists: SplicingCompass lists: deFuse lists: Assembly Based ReAligner lists: ggbio lists: miR-PREFeR lists: ALDEx2 lists: HTqPCR lists: NanoStringNorm lists: T-profiler lists: Snakemake lists: jmzTab lists: MIPgen lists: Bpipe lists: PoPoolation lists: L-Measure lists: MultiPhen lists: PheWAS R Package lists: InsertionMapper lists: Quantitative Enrichment of Sequence Tags lists: INMEX lists: Segway - a way to segment the genome lists: SeWeR - SEquence analysis using WEb Resources lists: TagDust lists: BSRD lists: DER Finder lists: Stem Cell Discovery Engine lists: Kdetrees lists: Tree and reticulogram REConstruction lists: BioPig lists: NCBI BioSystems Database lists: Distributed String Mining Framework lists: NEWT lists: PILGRM lists: Selectome: a Database of Positive Selection lists: SVMerge lists: Parseq lists: SVseq lists: Small Molecule Pathway Database lists: miRNAKey lists: DELLY lists: Apo and Holo structures DataBase lists: BioSample Database at EBI lists: MetaPhyler lists: MG-RAST lists: SLIQ lists: SOPRA lists: Information Hyperlinked Over Proteins lists: AmphoraNet lists: SINA lists: SSPACE lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: STING Report lists: G-BLASTN lists: RNA-eXpress lists: MethPipe lists: SoyBase lists: Strelka2 lists: RUM lists: SPOT - Biological prioritization after a SNP association study lists: VFS lists: PHAge Search Tool lists: MLTreeMap lists: SEECER lists: GeneTalk lists: ERANGE lists: rQuant lists: NCBO Annotator lists: ShoRAH lists: Yabi lists: ORMAN lists: FusionMap lists: CoPub lists: Scripture lists: SolexaQA lists: Kismeth lists: EMAGE Gene Expression Database lists: SAMStat lists: Knime4Bio lists: Bis-SNP lists: GobyWeb lists: Jellyfish lists: PRINSEQ lists: PASS lists: GSNAP lists: SOAPaligner/soap2 lists: MethylViewer lists: READSCAN lists: DistMap lists: MicrobesOnline lists: mrFAST lists: FLASH lists: TIGRFAMS lists: TMA Navigator lists: Bambino lists: TreQ lists: SeqMap lists: SeqTrace lists: TRANSFAC lists: GoFish lists: MethylomeDB lists: CLIPZ lists: SerbGO lists: ToppGene Suite lists: ngsTools lists: PePr lists: DMRforPairs lists: CharProtDB: Characterized Protein Database lists: Expression Profiler lists: SNPsandGO lists: GoSurfer lists: WEGO - Web Gene Ontology Annotation Plot lists: SOURCE lists: Stampy lists: DiseaseMeth lists: BLESS lists: GraphProt lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: Europe PubMed Central lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: DBETH - Database for Bacterial ExoToxins for Humans lists: VirHostNet: Virus-Host Network lists: GWASdb lists: HFV Database lists: HotRegion - A Database of Cooperative Hotspots lists: eQuilibrator lists: FunTree lists: Cascade lists: 959 Nematode Genomes lists: ICEberg lists: IndelFR - Indel Flanking Region Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: ProRepeat lists: NRG-CING lists: InterEvol database lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: Newtomics lists: MIPModDB lists: DistiLD - Diseases and Traits in LD lists: Polbase lists: UMD-BRCA1/ BRCA2 databases lists: ScerTF lists: VIRsiRNAdb lists: ProPortal lists: OGEE - Online GEne Essentiality database lists: RecountDB lists: PRED-GPCR lists: RNA CoSSMos lists: PRED-SIGNAL lists: SNPedia lists: SpliceDisease lists: HMM-TM lists: deepSNV lists: OMPdb lists: PRED-LIPO lists: VICUNA lists: Predictive Networks lists: COEUS lists: GeneTrail lists: epigenomix lists: ADGO lists: SRAdb lists: QCGWAS lists: Flycircuit lists: MouseBook lists: Immune Epitope Database and Analysis Resource (IEDB) lists: SitEx lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: TSSer lists: ATRHUNTER lists: Phytozome lists: Decombinator lists: ViralZone lists: COLT-Cancer lists: Gene Expression Database lists: BEDTools lists: waviCGH lists: Pseudomonas Genome Database lists: BIGpre lists: MyHits lists: CAPS Database lists: SpliceTrap lists: EagleView lists: IMGT/LIGM-DB lists: RIKEN integrated database of mammals lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: canSAR lists: GWAMA lists: AutismKB lists: zfishbook lists: PomBase lists: Myrna lists: PLEXdb - Plant Expression Database lists: RamiGO lists: PhenoM - Phenomics of yeast Mutants lists: IMGT/GENE-DB lists: HIstome: The Histone Infobase lists: SCOP: Structural Classification of Proteins lists: CuticleDB lists: agriGO lists: Expression Database in 4D lists: ESEfinder 3.0 lists: TriTrypDB lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: AgBase lists: Hyper Cell Line Database lists: Midbody, Centrosome and Kinetochore lists: Chromosome 7 Annotation Project lists: MfunGD - MIPS Mouse Functional Genome Database lists: Taipan lists: VISTA Browser lists: T1DBase lists: lobSTR lists: VISTA Enhancer Browser lists: MEROPS lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: Candidate Genes to Inherited Diseases lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: eTBlast lists: hiPathDB - human integrated Pathway DB with facile visualization lists: MuSiC lists: miRNEST lists: QuasiRecomb lists: neXtProt lists: DNAtraffic lists: BeeBase lists: NetOGlyc lists: GenoTan lists: GMAP lists: LegumeIP lists: SeqBuster lists: elastix lists: iMir lists: WEBLOGO lists: MaCH-Admix lists: Pathema lists: SNPinfo Web Server lists: MOSCPHASER lists: NEBcutter lists: Atlas2 lists: FGDP lists: Velvet lists: HomSI lists: MicroSNiPer lists: MIRA lists: ALLPATHS-LG lists: CUPSAT lists: SVDetect lists: omiRas lists: CopySeq lists: MutSig lists: HapFABIA lists: DIANA-LncBase lists: MutationTaster lists: HMCan lists: Geneious lists: kmer-SVM lists: SICER lists: ZINBA lists: Pedimap lists: MAnorm lists: PlantTFcat lists: MethMarker lists: NPS lists: PeakRanger lists: SEAL lists: OligoArray lists: PSAR-Align lists: CEQer lists: CloudBurst lists: nucleR lists: RACE lists: Asterias lists: PatMaN lists: RobiNA lists: LitInspector lists: Btrim lists: ArrayAnalysis.org lists: CANGS lists: GeneStitch lists: ProDesign lists: JiffyNet lists: AlienTrimmer lists: GenoREAD lists: HSLPred lists: CancerResource lists: FABIA lists: PlnTFDB lists: easyRNASeq lists: OBI-Warp lists: PREDDIMER lists: ECHO lists: ICPL ESIQuant lists: PRIDE Converter 2 lists: SlideSort-BPR lists: COBRApy lists: MFPaQ lists: TopHat-Fusion lists: miRPlant lists: SNP ratio test lists: compomics-utilities lists: PLEK lists: multiplierz lists: Allim lists: ISDTool lists: NetCoffee lists: MToolBox lists: Scalpel lists: DNaseR lists: LocalAli lists: NAIL lists: iceLogo lists: GPU-Meta-Storms lists: AMS lists: rqubic lists: ANNOVAR lists: A5-miseq lists: PhosphoSiteAnalyzer lists: Cell motility lists: MethylCoder lists: CAZy- Carbohydrate Active Enzyme lists: CPFP lists: GENE-counter lists: PoolHap lists: LOCAS lists: CloudAligner lists: HeurAA lists: Mouse Genome Database lists: MitoBreak lists: PolyPhen: Polymorphism Phenotyping lists: GSA-SNP lists: featureCounts lists: Crossbow lists: CSAR lists: seqMINER lists: BEADS lists: IUPHAR/BPS Guide to Pharmacology lists: QuantiSNP lists: Cube-DB lists: Death Domain database lists: psRNATarget lists: DSAP lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: GeneSigDB lists: MACS lists: NGSmethDB lists: GENSCAN lists: INCLUSive lists: MINAS - Metal Ions in Nucleic AcidS lists: Composition Profiler lists: NNcon lists: EGSEA lists: SCRATCH lists: Telescoper lists: Buccaneer lists: ProtTest lists: Morpheus lists: KAVIAR lists: DISEASES lists: SPEX2 lists: RAST Server lists: GeneWise lists: Crystallography and NMR System (CNS) lists: FATCAT lists: Membrane Protein Explorer lists: LTR_Finder lists: PALEOMIX lists: TISSUES lists: MetaMapR lists: primers4clades lists: MS-GF+ lists: PLAN2L lists: Off-Spotter lists: ProteomicsDB lists: CHiCAGO lists: SC3 lists: Bio-tradis lists: ApiDB CryptoDB lists: HISAT2 lists: PhyD3 lists: LoRDEC lists: Bamtools lists: ALTER lists: MultiQC lists: TFBS lists: EnrichmentMap lists: Poretools lists: Exonerate lists: 3D-footprint lists: Genesis lists: oligo lists: DISULFIND lists: Fastml lists: mentha lists: Oufti lists: eXpression2Kinases lists: IDEPI - IDentify EPItopes lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: TRANSIT lists: DINIES lists: Splicing Express lists: FluxModeCalculator lists: Lifebit Deploit lists: ngsRelate lists: SARTools lists: OmicsNet lists: SPICE lists: Microscopy Image Browser lists: Thunder STORM lists: clusterProfiler lists: NetworkAnalyst lists: ANOCVA lists: Rsubread lists: Subread lists: ConsensusClusterPlus lists: CIBERSORT lists: FRETBursts lists: CCTOP lists: scran lists: ScaffMatch lists: Heatmapper lists: Goseq lists: PRSice lists: UMI-tools lists: Proovread lists: BinPacker lists: JAMM lists: CentroidFold lists: ComplexHeatmap lists: PatchDock lists: FastProject lists: ExPASy ABCD database lists: Gigwa lists: shinyGEO lists: GeSeq lists: EMBOSSMatcher lists: Geneshot lists: Mousebytes lists: trimAl lists: AmoebaDB lists: STRUCTURE lists: PASTEClassifier lists: NetPhos lists: HiC-Pro lists: SWISS-MODEL lists: Blood Exposome Database lists: HingeProt lists: ChiCMaxima lists: ProtParam Tool lists: GalaxyRefine lists: FlowCal lists: SpydrPick lists: R/qtl2 lists: Roary lists: SIGNOR lists: Protein Interactions Calculator lists: REDIportal lists: MaxAlign lists: Minimap2 lists: PrognoScan lists: GPS-SUMO lists: Signaling Pathways Project lists: ProSA-web lists: GalaxyWEB lists: iTOL lists: EpiModel lists: rVista lists: AlgPred lists: D-GENIES lists: Robetta lists: GOnet lists: E-CRISP lists: STAMP lists: Batch Web CD-Search Tool lists: aroma.light lists: Annotree lists: Database of Secondary Structure Assignments lists: Clustal Omega lists: DESeq lists: discoSnp lists: vcflib lists: Genome BioInformatics Research Lab - gff2ps lists: Primer3 lists: BioPerl lists: Rainbow lists: RNAhybrid lists: Clustal W2 lists: Apollo lists: IgBLAST lists: Ray lists: khmer lists: Stacks lists: Predictions for Entire Proteomes lists: DIALIGN lists: EBSeq lists: Minia lists: SAMtools/BCFtools lists: Artemis: Genome Browser and Annotation Tool lists: NCBI BLAST lists: biobambam lists: VICMpred lists: Staden Package lists: Bowtie 2 lists: RAxML lists: WHAM lists: VarScan lists: Bismark lists: ea-utils lists: HTSeq lists: Vienna RNA lists: Regulatory Sequence Analysis Tools lists: BitSeq lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: HilbertVis lists: BRIG lists: Unipro UGENE lists: GBrowse lists: Sickle lists: AmpliconNoise lists: FreeBayes lists: tRNAscan-SE lists: CD-HIT lists: SSAKE lists: MACH lists: Segemehl lists: BEAST lists: Pscan-ChIP lists: cutadapt lists: Oases lists: CGView lists: SOAPsnp lists: T-Coffee lists: Kalign lists: Circos lists: Trinity lists: Flexbar lists: SIFT lists: ProbCons lists: OpenMS lists: RSEM lists: Glimmer lists: GROMACS lists: CummeRbund lists: edgeR lists: DNAcopy lists: TopHat lists: SortMeRNA lists: LIMMA lists: AMOS lists: Cufflinks lists: Nanopolish lists: GMA lists: Prokka lists: phyloseq lists: SeqPrep lists: precrec lists: Atac lists: PAML lists: KisSplice lists: StoatyDive lists: IMGT-ONTOLOGY lists: KAT lists: SeaView lists: FastTree lists: Crux tandem mass spectrometry analysis software lists: rCASC lists: minet lists: becas lists: tximport lists: globaltest lists: CheckM lists: BLINK lists: mosdepth lists: bwtool lists: dcmqi lists: Pilon lists: ASHLAR lists: metagen lists: COPASI lists: BUSCO lists: bridge lists: TGS-GapCloser lists: NiftyPET lists: Blobtools lists: THESIAS lists: Fcirc lists: chimerascan lists: GLUE lists: SwiftOrtho lists: HaploReg lists: ScanITD lists: andi lists: metahdep lists: ImaGene lists: Jalview lists: MeroX lists: qrqc lists: BioNix lists: MiXCR lists: casper lists: libmgf lists: sleuth lists: imDEV lists: miRDB lists: yaqcaffy lists: NiftyFit lists: mlgt lists: SMARTdenovo lists: HH-suite lists: StatAlign lists: affy lists: shovill lists: Fiji lists: Racon lists: rbsurv lists: quantsmooth lists: tensorflow lists: seqbias lists: ngs.plot lists: bsseq lists: MGnify lists: dyebias lists: h5vc lists: ascat lists: Cuffdiff lists: mitopred lists: OrthoFinder lists: PIRATE lists: Bridger lists: Eoulsan lists: VEnCode lists: eTRIKS lists: fracridge lists: lumi lists: genomation lists: Hippocampome.org lists: SymPy lists: icy lists: GADMA lists: HaTSPiL lists: XL-mHG lists: ropls lists: scanpy lists: MethBase lists: sabre lists: plgem lists: MyGene.info lists: CRISPRcasIdentifier lists: biobakery lists: VETA lists: EpiEstim lists: HyPhy lists: ODAM lists: BISE lists: docker4seq lists: qcmetrics lists: Pavian lists: genehunter-imprinting lists: smashpp lists: NanoSim lists: SimVascular lists: BSA4Yeast lists: minfi lists: TDimpute lists: RepeatScout lists: neuroelectro lists: MRIcron lists: RepeatFiller lists: ShinyLearner lists: CRISPR-ERA lists: CRISPR-P lists: Warp lists: GEMINI lists: MAFFT lists: TransDecoder lists: Phenoscape lists: PhenoMeNal lists: les lists: Laniakea lists: CandiMeth lists: eisa lists: ProP Server lists: ggtree lists: scVelo lists: PathwayMatcher lists: charm lists: Telescope lists: skewer lists: multtest lists: Human Neocortical Neurosolver lists: beadarray lists: BioBERT lists: PlotTwist lists: GraphClust2 lists: METAREP lists: QIIME lists: halSynteny lists: scater lists: Galaxy scater lists: larvalign lists: iontree lists: VAPPER lists: GENCODE lists: Datanator lists: Bio2BEL lists: UALCAN lists: ffpe lists: MCScan lists: VisR lists: Metascape lists: GemSIM lists: EvidenceFinder lists: pepwheel lists: RDXplorer lists: bcbio-nextgen lists: OpenWorm lists: ActiveDriver lists: QuickNII lists: timecourse lists: Bionitio lists: ggplot2 lists: TCW lists: SPM lists: pvac lists: GeneMarkS-T lists: ascend lists: RatMine lists: CRISPRdirect lists: phantompeakqualtools lists: prank lists: refgenie lists: NanoPipe lists: vsn lists: PAFScaff lists: odMLtables lists: biospytial lists: NeuroChaT lists: clustergrammer lists: glycomedb lists: CLIP-Explorer lists: pheatmap lists: EnteroBase lists: GigaSOM.jl lists: bio.tools lists: SPP lists: lapmix lists: EHRtemporalVariability lists: HmtVar lists: SnpHub lists: Online Peri-Event Time Histogram for Open Ephys lists: NMRProcFlow lists: QGIS lists: Flye lists: kallisto lists: clipcrop lists: cn.mops lists: UniCarbKB lists: pickgene lists: PsyGeNET lists: seq-annot lists: PASA lists: ReadqPCR lists: breseq lists: e-Driver lists: sim4cc lists: PhylomeDB lists: fastqz lists: PerM lists: rnaQUAST lists: NCBI BioProject lists: PEMer lists: metabnorm lists: FusionCatcher lists: STAR lists: VCFtools lists: UniCarb-DB lists: NormqPCR lists: SnpEff lists: DecGPU lists: gprege lists: VirusMINT lists: nondetects lists: circlize lists: SAMTOOLS lists: Neuroscience Information Framework lists: Dali Server lists: IRanges lists: dbEST lists: Genomic Ranges lists: eProbalign lists: Cistrome lists: DIANA-mirPath lists: BpForms lists: GenomicFeatures lists: SOAPdenovo lists: BcForms lists: 4See lists: ABNER lists: A Classification of Mobile genetic Elements lists: Addgene lists: BadMedicine lists: ADMIXMAP lists: ADMIXTOOLS lists: ALCHEMY lists: AETIONOMY lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: ALBERT lists: ALOHOMORA lists: Alternate splicing gallery lists: Allele Frequencies in Worldwide Populations lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ape lists: Alta-Cyclic lists: Assisted Model Building with Energy Refinement (AMBER) lists: Aroma.affymetrix lists: ANDES lists: ASSOCIATIONVIEWER lists: ArrayMiner lists: ASPEX lists: The Alternatve Splicing Database lists: AutoAssemblyD lists: AutoDock Vina lists: BAIT lists: BamView lists: Avogadro lists: ArrayPipe lists: Athena lists: BLAT lists: BARS lists: BayesEpiModels lists: BatMeth lists: BeetleBase lists: BBSeq lists: naiveBayesCall lists: BarraCUDA lists: BCBtoolkit lists: BioConda lists: BAR lists: BiG-SLiCE lists: SVM based method for predicting beta hairpin structures in proteins lists: betaVAEImputation lists: BiNGO: A Biological Networks Gene Ontology tool lists: Bioinformatics Toolkit lists: BioCarta Pathways lists: Biopieces lists: Bio++ lists: BioPlex lists: BioSimulations lists: BRAIN lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: biomaRt lists: bioSyntax lists: Bionimbus lists: BioSimulators lists: bioRxiv lists: Breakpointer lists: CiLiQuant lists: BSVF lists: BS Seeker lists: Bs-Seeker2 lists: BWA lists: CARD lists: Canu lists: Cell Image Library (CIL) lists: BRB-ArrayTools lists: CATALYST lists: CATH: Protein Structure Classification lists: CAT lists: CEM lists: CASPAR lists: CHEBI lists: ChimeraSlayer lists: CATdb: a Complete Arabidopsis Transcriptome database lists: ChemSpider lists: Chipster lists: CCREL lists: cisTEM lists: circlncRNAnet lists: Centrifuge Classifier lists: Cancer Genome Anatomy Project lists: ChIPMunk lists: Chromas lists: CiteFuse lists: CRCView lists: ChiRA lists: ClinVar lists: ClinTrajAn lists: clustLasso lists: CleanEx lists: Clinotator lists: CNVer lists: ComiR lists: CODEHOP lists: ClustVis lists: Comparative Metatranscriptomics Workflow lists: CMap lists: CorMut lists: CNV-seq lists: Coot lists: CITE-seq-Count lists: CoCo lists: CopyDetective lists: Chromosome Scale Assembler lists: cortex lists: ConDeTri lists: CRISPy-web lists: CONTRA lists: CovalentDock Cloud lists: CUDASW++ lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: DANPOS2 lists: DOGMA lists: CorrDrugTumorMSI lists: DAMBE lists: D-EE lists: CoryneRegNet lists: ΔG prediction server lists: DIAMOND lists: CYANA lists: Datasets2Tools lists: DEXSeq lists: DichroWeb lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: DBTSS: Database of Transcriptional Start Sites lists: dbSNP lists: DiffBind lists: DETONATE lists: DiProGB lists: Descriptions of Plant Viruses lists: DIME lists: DicomTypeTranslator lists: CSDeconv lists: Dictyostelium discoideum genome database lists: DSK lists: DGIdb lists: DisProt - Database of Protein Disorder lists: DOMINE: Database of Protein Interactions lists: eDMR lists: ECLIPSE lists: Experimental Design Assistant lists: Dissect lists: Evolutionary Couplings Server lists: Enrichr lists: ensembldb lists: European Genome phenome Archive lists: EBCall lists: Ensembl Genomes lists: EMAN lists: ENIGMA lists: DISENTANGLER lists: Entrez Gene lists: Ensembl lists: eQtlBma lists: EpiGRAPH lists: EpiDISH R package lists: Examl lists: epitopepredict lists: DrivAER lists: Variant Effect Predictor lists: Epigenomics Workflow on Galaxy and Jupyter lists: Eukaryote Genes lists: Evex lists: FateID lists: EXOMEPICKS lists: European Variation Archive (EVA) lists: FANTOM DB lists: Genome Annotation Generator lists: FireDB lists: FGENESH lists: FluoRender lists: FLOSS lists: fineSTRUCTURE lists: FastQC lists: FINDbase Worldwide lists: ExpressYourself lists: fgsea lists: FuncAssociate: The Gene Set Functionator lists: NHLBI Exome Sequencing Project (ESP) lists: FlyBase lists: FlexProt: flexible protein alignment lists: GASV lists: Fugu Genome Project lists: Full-Length cDNA Database lists: FragGeneScan lists: FunRich: Functional Enrichment analysis tool lists: FlowSOM lists: GASSST lists: GeMoMa lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: GEDIT lists: VBASE2 lists: Genome Database for Rosaceae lists: GenePattern Notebook lists: G-Mo.R-Se lists: FusionHunter lists: Genome Projector lists: GeneCodis lists: GEN3VA lists: GENERECON lists: GEMB lists: GeCo3 lists: Gene3D lists: Genomic Annotation in Livestock for positional candidate LOci lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: Genome Reviews lists: GATK lists: FunCluster lists: GFINDer: Genome Function INtegrated Discoverer lists: GermOnline lists: GeneSeeker lists: Gmove lists: Genometa lists: GensearchNGS lists: HARSH lists: Gibbs Motif Sampler lists: Generic GO Term Mapper lists: Genomedata lists: GMcloser lists: GEO2R lists: Gramene lists: Genome Aggregation Database lists: GoMapMan lists: GEPAT lists: Git lists: GNUMAP lists: Generic GO Term Finder lists: Graph2GO lists: Gene Ontology lists: Gaggle lists: GO2MSIG lists: GRASS lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: Genovar lists: HASTE-project lists: H-InvDB lists: Homologous Sequences in Ensembl Animal Genomes lists: Google lists: IMGT/HLA lists: Human Gene Mutation Database lists: GTDB-Tk lists: G protein receptor interaction feature finding instrument lists: HubMed lists: HPEPDOCK Server lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: HAPLOCLUSTERS lists: HiCUP lists: International HapMap Project lists: HiPipe lists: HTR lists: HINT lists: Hybrid-denovo lists: HS-TDT lists: Human Gene Connectome Server lists: HSSP lists: iDASH lists: hyfi: software suite for binding site search lists: HUDSEN lists: IMGT/StatClonotype lists: I-TASSER lists: ImJoy lists: IMEx - The International Molecular Exchange Consortium lists: IMG System lists: HCLUST lists: Human Splicing Finder lists: lme4 lists: Identifiers.org lists: IPD - Immuno Polymorphism Database lists: IntEnz- Integrated relational Enzyme database lists: IBIS: Inferred Biomolecular Interactions Server lists: IMGT - the international ImMunoGeneTics information system lists: Integr8 : Access to complete genomes and proteomes lists: IMGT HighV-QUEST lists: Isaac lists: Interolog/Regulog Database lists: InterProScan lists: IRESite lists: IPI lists: inGAP lists: ISFinder lists: KGGSeq lists: iPiG lists: IsoLasso lists: J-Express lists: JGI Genome Portal lists: IsaCGH lists: lncRNAdb lists: LDSELECT lists: IsoEM lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: IMG lists: LTR_FINDER_parallel lists: LAST lists: MBGD - Microbial Genome Database lists: jmzML lists: OntoQuest lists: LOCUSMAP lists: MaizeGDB lists: long-read-tools lists: LRPath lists: Magic lists: LS-SNP/PDB lists: LOCATE: subcellular localization database lists: Mammalian Gene Collection lists: Machado lists: MACiE lists: Maqview lists: LitMiner lists: MAKER lists: MEBS: Multigenomic Entropy-Based Score lists: MapSplice lists: Mascot lists: mapDamage lists: MEGAHIT lists: Metabolomics Workbench lists: Libra lists: ML Repo lists: MARRVEL lists: Maq lists: MentaLiST lists: MB-GAN lists: MetaCyc lists: MAP lists: MeQA lists: Metastats lists: MatrixDB lists: MetAMOS lists: MeRIP-PF lists: MendelIHT.jl lists: metaXplor lists: lsa_slurm lists: MetaCyto lists: UEA sRNA Workbench lists: MetaVelvet lists: MMAPPR lists: MBCluster.Seq lists: MIP Scaffolder lists: MERMAID lists: MobiDB lists: MPDA lists: MaSuRCA lists: MICSA lists: MIRIAM Resources lists: miROrtho: the catalogue of animal microRNA genes lists: NCBI lists: proMODMatcher lists: miRBase lists: MethylExtract lists: SCIPION lists: MPscan lists: mirTools lists: MISA lists: MP3 tool lists: Mspire-Simulator lists: Multi-omics Visualization Platform lists: mrCaNaVaR lists: MoDIL lists: MultiLoc lists: MULTIDISEQ lists: Noncoding RNA database lists: MRFSEQ lists: MizBee lists: Multiple Myeloma survival predictor lists: Mouse Phenome Database (MPD) lists: Nucleic Acid Database lists: Myriads lists: miRpathDB lists: MUMmer lists: mzMatch lists: NeLS lists: NEST Simulator lists: MutPred lists: NEMBASE lists: Open Babel lists: NetMHCpan Server lists: MULTIMAP lists: NCBI Genome Workbench lists: Nephele lists: NCBI Probe lists: Ngmlr lists: Necklace lists: NetNGlyc lists: NucleoFinder lists: NeuroMatic lists: Genotyping lists: NGSView lists: NOrMAL lists: Opera lists: NURD lists: ngLOC lists: NeSSM lists: NanoGalaxy lists: ObjTables lists: nmrML lists: nsSNPAnalyzer lists: OsiriX Medical Imaging Software lists: parSMURF lists: Open Trials lists: Ngs backbone lists: PartiGeneDB lists: Pfam lists: Oncodrive-fm lists: Online Resource for Community Annotation of Eukaryotes lists: PanoramaWeb lists: Omics Data Paper Generator lists: Pathway Tools lists: PDBe - Protein Data Bank in Europe lists: Pash 3.0 lists: Orientations of Proteins in Membranes database lists: Pathbase lists: PEDHUNTER lists: PAZAR lists: Peakzilla lists: PeakAnalyzer lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers lists: Pedigree-Draw lists: OLego lists: Parliament2 lists: PEDIGREEQUERY lists: PeakSeq lists: PEDPEEL lists: PhaseME lists: PHI-base lists: PHYLIP lists: PDB Finder lists: Phylogeny.fr lists: PRICE lists: PennSeq lists: Illuminating the Druggable Genome lists: Philius lists: Phenotypes and eXposures Toolkit lists: PhyloPat lists: PicTar lists: Eddy Lab Software lists: Protein Information Resource lists: PhyML lists: PhenoMan lists: PeptideAtlas lists: PIRSF lists: Polygenic Pathways lists: PLANTTFDB lists: pNovo+ lists: PLINK/SEQ lists: PEMA lists: pFind Studio: pLink lists: PM4NGS lists: PrimerBank lists: ProSight Lite lists: PolymiRTS lists: Phospho.ELM lists: Plant Co-expression Annotation Resource lists: Rampart lists: Protein Prospector lists: ProteomeXchange lists: PRED-TMBB lists: Proteomics Identifications (PRIDE) lists: PS-Plant Framework lists: ProtChemSI lists: PRADA lists: Pyntacle lists: PubCrawler lists: ProfCom - Profiling of complex functionality lists: PrimerSeq lists: PyBEL lists: PubChem lists: PubGene lists: R/QTLBIM lists: QGene lists: QMSIM lists: QmRLFS-finder lists: PolyPhred lists: QSRA lists: Preseq lists: ReactomePA lists: QuickGO lists: QUMA lists: RAREMETAL lists: REDItools lists: The Human Protein Atlas lists: rSNP Guide lists: PyRosetta lists: RefSeq lists: RaptorX lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: RegulonDB lists: RESID lists: R Project for Statistical Computing lists: Reactome lists: Rdisop lists: RepeatModeler lists: RESCUE-ESE lists: Relate lists: Reptile lists: R-SAP lists: riborex lists: RNA-SeQC lists: QuPath lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: RADAR-base lists: RiboTaper lists: SAMMate lists: rna-stability lists: RightField lists: SASGENE lists: RNAplex lists: runBioSimulations lists: ResponseNet lists: SilkDB lists: Scansite lists: Research-tested Intervention Programs (RTIPs) lists: sapFinder lists: SeqtrimNEXT lists: RNA Virus Database lists: SALT lists: SEEK lists: Seqtk lists: REDfly Regulatory Element Database for Drosophilia lists: SAFA Footprinting Software lists: SeqExpress lists: ROMPREV lists: SeqSaw lists: SeqEM lists: SHELX lists: rSeq lists: SHARCGS lists: rnaSPAdes lists: SimSeq lists: SGA lists: Sherman lists: SeQuiLa lists: SGD lists: ShinyGO lists: SISYPHUS lists: SVA lists: ASC lists: SIMULATE lists: SILVA lists: SNP HITLINK lists: SIBLINK lists: SKAT lists: SimRare lists: SnoopCGH lists: SMRT View lists: SASQUANT lists: SIMPED lists: Sniffles lists: SIBMED lists: SMI Services lists: SOAPnuke lists: SGN lists: SIDER lists: SMART lists: ShortFuse lists: SWEEP lists: SnpSift lists: SOAPfusion lists: SNPTEST lists: SwissTree lists: TopFIND lists: Solas lists: SoupX lists: STEPS lists: FASTSLINK lists: SpliceMap lists: StSNP lists: Supersplat lists: Sybil lists: TAPIR: target prediction for plant microRNAs lists: SWISS-2DPAGE lists: SISSRs lists: T-lex lists: SUMSTAT lists: TAGS lists: Spot lists: TDR Targets Database lists: TDT-PC lists: SpoTyping lists: SynTView lists: SynergyFinder lists: TRAL lists: SPIKE lists: Transporter Classification Database lists: TransmiR lists: TASSEL lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: FLUX CAPACITOR lists: TB PORTALS lists: TAndem Splice Site DataBase lists: VirusHunter lists: topGO lists: TMAJ lists: ApiDB ToxoDB lists: tradeSeq lists: TreeDyn lists: Trans-ABySS lists: IQ-TREE lists: Biological General Repository for Interaction Datasets (BioGRID) lists: Trowel lists: TomoMiner lists: UTRdb/UTRsite lists: TWOLOC lists: V-Phaser 2 lists: TropGENE DB lists: Trim Galore lists: TRACESPipe lists: Gene Index Project lists: Tool recommender system in Galaxy lists: WEIGHTED FDR lists: UTGB Toolkit lists: xia2 pipeline lists: USeq lists: TRiCoLOR lists: UniParc lists: VAAST lists: variancePartition lists: VirusSeq lists: Webproanalyst lists: XPN lists: WSsas - Web Service for the SAS tool lists: UNAFold lists: zUMIs lists: VaDiR lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: Vector Alignment Search Tool lists: Zebrafish Information Network (ZFIN) lists: YASARA lists: Vmatch lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Xenbase lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: AutoDock lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: SUP lists: Trimmomatic lists: VIPERdb lists: ABySS lists: AdapterRemoval lists: Alien-hunter lists: ALTree lists: Integrative Genomics Viewer lists: RDKit: Open-Source Cheminformatics Software lists: Acacia lists: AMAP lists: Anfo lists: Aragorn lists: Arden lists: Ariba lists: ART lists: Augustus lists: Axe lists: Baitfisher lists: BALLView lists: BEAGLE lists: BEDOPS lists: eXpress lists: BOXSHADE 3.21 lists: Cassiopee lists: Cdbfasta lists: Circlator lists: Clearcut lists: Clonalframe lists: ClonalOrigin lists: Computational Morphometry Toolkit lists: Concavity lists: CRAC lists: cwltool lists: Daligner lists: Datamash lists: DNACLUST lists: DWGSIM lists: Eigensoft lists: EMBOSS lists: ESTScan lists: EULER-SR lists: FASTLINK lists: FigTree lists: fitGCP lists: Fsm-lite lists: Gamgi lists: GASiC lists: Ghemical lists: GIIRA lists: Grinder lists: Gwyddion lists: Hmmer lists: HTQC lists: IDBA-UD lists: ImageJ lists: Infernal lists: PyMOL lists: GenABEL lists: Biopython lists: QuorUM lists: Prodigal lists: QuteMol lists: PRESTO: Genetic Association Analysis Software lists: Probalign lists: Computational Structural Biology Toolbox lists: LEfSe lists: Happy lists: jModelTest lists: KMC lists: LAMARC lists: libRoadRunner lists: LoFreq lists: MetaPhlAn lists: MicrobiomeUtilities lists: MINIMAC lists: MIPE lists: mothur lists: Mugsy lists: GNU Octave lists: Oncofuse lists: PBSIM lists: PerlPrimer lists: PHAST lists: Picard lists: PLINK lists: ADEGENET lists: phytools lists: PSCBS lists: R/QTL lists: SAM lists: vegan lists: RepeatMasker lists: Scythe lists: SEER lists: Seq-Gen lists: SMRT-Analysis lists: Scalable Nucleotide Alignment Program lists: SPAdes lists: TraceTuner lists: Transterm lists: TreeView lists: Viewmol lists: Vascular Modeling Toolkit lists: Aegean lists: amide lists: Anndata lists: ANTS - Advanced Normalization ToolS lists: ARB project lists: ArtificialFastqGenerator lists: Arvados lists: Bandage lists: Berkeley Advanced Reconstruction Toolbox lists: BBmap lists: Eagle lists: Bio-Formats lists: BioImage Suite lists: BioJava Project lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis lists: BRAKER lists: Bustools lists: Computerized Anatomical Reconstruction and Editing Toolkit lists: CellProfiler Image Analysis Software lists: ChIPSeq Peak Finder lists: ChromHMM lists: Cluster lists: Cytoscape lists: Dazzler lists: DCMTK: DICOM Toolkit lists: DeepNano lists: dinifti lists: DICOMscope lists: Dipy lists: Drop-seq tools lists: Electronic Cell Project lists: Ecopcr lists: Edtsurf lists: DOMAINATRIX lists: DOMALIGN lists: Embassy-domsearch lists: E-mem lists: e-PCR lists: Falcon lists: Fastaq lists: Fastqtl lists: Ffindex lists: FreeSurfer lists: FSA lists: FSL lists: Galaxy lists: GARLI lists: Garlic lists: IndelGenotyper lists: gdpc lists: Gemma lists: GenomeTools lists: Gentle lists: GERP lists: Gff2aplot lists: gffread lists: GraPhlAn lists: Gubbins lists: Harvest-tools lists: HiLive lists: Hinge lists: ImageMagick lists: ImageVis3D lists: Indelible lists: InVesalius 3 lists: IQ TREE lists: ITK-SNAP lists: JBrowse lists: JIST: Java Image Science Toolkit lists: Fastahack lists: Lipsia lists: LUMPY lists: Mash lists: Mesquite lists: MetaBAT lists: MOSAIK lists: MRtrix lists: Human Disease Ontology lists: NanoFilt lists: Object-Oriented Development Interface for NMR lists: OpenElectrophy lists: OpenMEEG lists: OpenWalnut lists: OptiType lists: PARASAIL lists: ParaView lists: PhyloPhlAn lists: Phyutility lists: Porechop lists: PSIPRED lists: PsychoPy lists: Pychopper lists: pydicom lists: PySurfer lists: MNE software lists: pbcore lists: pyxnat lists: QIIME2 lists: RAxML Next Generation lists: ShortRead lists: Phangorn lists: psych lists: VennDiagram lists: Recognition of Errors in Assemblies using Paired Reads lists: RELION lists: RStudio lists: Salmon lists: Scoary lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Short Read Sequence Typing for Bacterial Pathogens lists: Umap lists: VoxBo lists: WTDBG lists: XNAT - The Extensible Neuroimaging Archive Toolkit lists: ABACAS lists: AceDB lists: LINKAGE lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: RSEM lists: Aeskulap lists: alleleCount lists: assembly-stats lists: Atropos lists: Assemblytics lists: Augur lists: AxParafit lists: Aghermann lists: bambamc lists: AxPcoords lists: bamkit lists: BAli-Phy lists: Auspice lists: BBHash lists: BCALM 2 lists: Bibus lists: BioMAJ lists: BioCocoa lists: Biber lists: BioImageXD lists: caftools lists: BOLT-LMM lists: CamiTK lists: CLI for BioMAJ lists: CAMP lists: CAT and BAT lists: CHIME lists: CDK lists: ChromImpute lists: CiftiLib lists: conda-package-handling lists: CARD lists: CONTRAfold lists: CodonW lists: Change-O lists: C Thread Pool lists: Chemtool lists: covtobed lists: CTK lists: CTDopts lists: CTDConverter lists: Conquest DICOM lists: CTSim lists: Dicom3tools lists: Dendroscope3 lists: cyvcf2 lists: Deepbinner lists: EDFlib lists: EDFbrowser lists: dicompyler lists: EMMAX lists: DEXTRACTOR lists: DNApi lists: Epigrass lists: ELPH lists: ExaBayes lists: EMPeror lists: FreeImage lists: Fast5 Library lists: Entangle lists: FFP lists: GenomeTester4 lists: Filtlong lists: EMBOSS explorer lists: GfaPy lists: GATB lists: GCLib lists: EpiFire lists: HTSJDK lists: GDCM lists: GNUmed lists: GraphMap2 lists: foreign lists: Ginkgo CADx lists: GramAlign lists: IDeFIX lists: ImageTooth lists: Htscodecs lists: IGoR lists: iVar lists: InsPecT lists: Intake lists: IgDiscover lists: JAligner lists: ISMRMRD lists: JabRef lists: Lambda lists: Kaptive lists: KBibTeX lists: InSilicoSeq lists: kineticsTools lists: AcePerl lists: KmerResistance lists: Bio-EUtilities lists: Insight Toolkit lists: Kleborate lists: KMA lists: kempbasu lists: Bio-ASN1-EntrezGene lists: IVA lists: Bio-Coordinate lists: Bio-Graphics lists: AI-FANN lists: Bio-Chado-Schema lists: BioD lists: Bio-Tools-Run-Alignment-Clustalw lists: Bio-PrimerDesigner lists: Bioparser lists: Edlib lists: Bio-SamTools lists: libdisorder lists: libncl lists: Bio-Tools-Run-Alignment-TCoffee lists: Chado lists: Bio-Tools-Phylo-PAML lists: libGDF lists: JLODA lists: libdivsufsort lists: libminc lists: Bio-SCF lists: Sort-Key-Top lists: Java NeXML libraries and tools lists: libmaus2 lists: libqes lists: MIA lists: libics lists: FAST Analysis of Sequences Toolbox lists: Libchipcard lists: TaxonomyTree lists: Core Wrapper lists: Lighter lists: SSW Library lists: libqc++ lists: SeqLib lists: tabixpp lists: libStatGen lists: ThreadPool lists: Lucy lists: MafFilter lists: Metastudent lists: Libxdf lists: limereg lists: Mapsembler2 lists: MAXFLOW lists: metaBIT lists: MacSyFinder lists: VIGRA lists: MCL lists: MHAP lists: MindTheGap lists: Logol lists: medicalterms lists: mmtf-python lists: Miniasm lists: Tab2MAGE lists: MView lists: LTRsift lists: Molekel lists: mirtop lists: Maude lists: MicrobeGPS lists: mPSQed lists: mPTP lists: SMILE lists: Entrez Direct lists: NW-align lists: NanoSV lists: Mustang lists: Nanocall lists: Ngila lists: MRtrix3 lists: NORSp lists: Murasaki lists: Nextflow lists: NCBI accession download script lists: omegaMap lists: NJplot lists: NanoLyse lists: OpenCFU lists: NORSnet lists: OBITools lists: NeoBio lists: OptimiR lists: PartitionFinder lists: OpenSurgSim lists: NanoPlot lists: NextSV lists: OpenEMR lists: Orthanc lists: PAIPline lists: Odil lists: PHYLOViZ lists: PlasmidSeeker lists: PDB2PQR lists: OpenIGTLink lists: Parsnp lists: parallel-fastq-dump lists: ParsInsert lists: PiGx-RNAseq lists: PfTools lists: PlasmidID lists: Phyx lists: pipasic lists: pngquant lists: pbcopper lists: Patristic lists: PLIP lists: Placnet lists: PhySamp lists: pufferfish lists: PRINSEQ lists: PLAST lists: PCMA lists: picopore lists: POA lists: PROFisis lists: ProDA lists: PRANK lists: Cooler lists: pyepl lists: pssh2 lists: Plastimatch lists: pynast lists: psignifit lists: python-airr lists: Populations lists: pyFAI lists: python-biom-format lists: pyranges lists: purple lists: PyCogent lists: qtlreaper lists: qcumber lists: python-bx lists: pyomo lists: pycoqc lists: Proteinortho lists: DendroPy lists: qtltools lists: pyscanfcs lists: rambo-k lists: qcat lists: rasmol lists: rampler lists: raccoon lists: ragout lists: rapmap lists: quicktree lists: Raster3D lists: AnnotationHub lists: Rate4Site lists: altcdfenvs lists: annotate lists: biomformat lists: Biobase lists: affyio lists: bridgedbr lists: BiocGenerics lists: biovizBase lists: genefilter lists: CNEr lists: bsgenome lists: geneplotter lists: ctc lists: genomicalignments lists: go.db lists: genomeinfodb lists: hypergraph lists: gviz lists: groHMM lists: mergeomics lists: impute lists: makecdfenv lists: multiassayexperiment lists: qusage lists: mutationalpatterns lists: metagenomeseq lists: preprocesscore lists: pwmenrich lists: rbgl lists: htsfilter lists: nanostringqcpro lists: rgsepd lists: rcpi lists: pcaMethods lists: adephylo lists: rsamtools lists: savr lists: tfbstools lists: xvector lists: ade4 lists: biwt lists: beeswarm lists: cmprsk lists: alakazam lists: bio3d lists: Epi lists: BoolNet lists: DT lists: DoseFinding lists: itertools lists: fitdistrplus lists: fitbitscraper lists: dynamicTreeCut lists: epibasix lists: distory lists: forecast lists: incidence lists: hms lists: nmf lists: mediana lists: genetics lists: lexrankr lists: psychometric lists: optimalcutpoints lists: proc lists: pcapp lists: parmigene lists: rann lists: phylobase lists: psyphy lists: psychotree lists: rnexml lists: rook lists: rpact lists: tigger lists: robustrankaggreg lists: qqman lists: rwave lists: shazam lists: rsvd lists: rncl lists: rotl lists: rniftilib lists: sjplot lists: wavethresh lists: stringi lists: snowfall lists: waveslim lists: surveillance lists: tsne lists: webgestaltr lists: resfinder lists: readucks lists: recan lists: roadtrips lists: readseq lists: roguenarok lists: rtax lists: rgfa lists: ruby-bio lists: runcircos-gui lists: sailfish lists: samclip lists: saint lists: sambamba lists: seqmagick lists: sbmltoolbox lists: seq-seq-pan lists: seqsero lists: seqwish lists: shapeit4 lists: sepp lists: crb-blast lists: sigma-align lists: sibsim4 lists: signalalign lists: sibelia lists: shiny-server lists: sistr lists: skesa lists: sigviewer lists: snpomatic lists: spaced lists: sitplus lists: sofa-apps lists: sra-toolkit lists: strap-base lists: sparta lists: swarm lists: sourmash lists: surankco lists: streamlit lists: tab2mage lists: sumaclust lists: sweed lists: tacg lists: zAlign lists: tiddit lists: Workrave lists: sprai lists: VolPack lists: XMedCon lists: Yanosim lists: Yanagiba lists: libswiss-perl lists: yaha lists: VisIt lists: VelvetOptimiser lists: variation graph lists: vcfanno lists: VarMatch lists: VirulenceFinder lists: CCS lists: VADR lists: VARNA lists: VMD lists: FISH lists: trace2dbEST lists: TREE-PUZZLE lists: umis lists: Trinculo lists: toil lists: TRANSIT lists: toppred lists: Unicycler lists: TM-align lists: Tn-seq explorer lists: Tombo lists: TopHat-Recondition is related to: FreeContact is parent organization of: neurodebian			Free, Freely available	nlx_151598			SCR_006638	Debian - The universal operating system, Debian GNU/Linux	2026-09-12 12:56:43	52
Genetic Analysis Software Resource Report Resource Website 1+ mentions	Genetic Analysis Software (RRID:SCR_013155)	GAS	catalog, data or information resource, data set, database, software resource	THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.	gene mapping, gene, genetic, genomic, model, modeling, software program, genetic linkage analysis, qtl analysis, genetic marker order, genetic association analysis, haplotype construction, pedigree drawing, population genetics	is used by: NIF Data Federation lists: EM-DECODER lists: ENTROPY BLOCKER lists: SOAP lists: ADEGENET lists: 2LD lists: SQTL lists: POLYMORPHISM lists: EDAC lists: FEST lists: GENEHUNTER SAD lists: COMDS lists: CHAPLIN lists: CRIMAP lists: DCHIP LINKAGE lists: FLOSS lists: HAP 1 lists: HAPSCOPE lists: LDB/LDB+ lists: LOCUSMAP lists: MRH lists: PEDIGREE-VISUALIZER lists: PEDPHASE lists: QTL CAFE lists: RHMAPPER lists: R/GC, R/GCF lists: R/GWAPOWER lists: R/WEIGHTED FDR lists: SIMM lists: SOLAR lists: TDTHAP lists: HWESTRATA lists: TDT-PC lists: EQTL EXPLORER lists: GAS2 lists: LDMET lists: LAMBDAA lists: EIGENSOFT/EIGENSTRAT lists: Happy lists: LAMP lists: CLUSTAG lists: OSA lists: SIMIBD lists: SNPSTATS lists: Haploview lists: QGene lists: PAWE-3D lists: MILD lists: PEDPLOT lists: GS-EM lists: PEDSCRIPT lists: Multipoint Identical-by-descent Method lists: PARENTE lists: Integrated Software lists: PEDRAW/WPEDRAW lists: POPDIST lists: TDTASP lists: TDTPOWER lists: TDT/S-TDT lists: HAPLOBLOCKFINDER lists: HAPMIXMAP lists: Genotype-IBD Sharing Test lists: LDGROUP lists: LDHAT lists: LDMAP lists: LDHEATMAP lists: LDSELECT lists: LINKAGE lists: LDSUPPORT lists: FASTLINK lists: LINKAGE - CEPH lists: LSP lists: Whap lists: TREESCAN lists: Graphical Overview of Linkage Disequilibrium lists: MAIA lists: MULTIMAP lists: R/ADEGENET lists: R/ENTROPY BLOCKER lists: BEAM lists: BMAPBUILDER lists: POPGEN lists: RTDT lists: R/SPECTRAL-GEM lists: R/STEPWISE lists: HAPLOCLUSTERS lists: TKMAP lists: CLUMP lists: FAMOZ lists: INTEGRAYEDMAP lists: SIBMED lists: POOLSCORE lists: LDA lists: LAPSTRUCT lists: BETA lists: ALTree lists: TRANSMIT lists: ETDT lists: R/TDTHAP lists: RVTESTS lists: S lists: ET-TDT lists: ILR lists: MAPCREATOR lists: MAPMAKER/SIBS lists: MAP MANAGER QT lists: MGA-MAPF2 lists: Pedigree-Draw lists: FASTMAP (1) lists: ASPEX lists: PEDJAVA lists: PEDPEEL lists: SIMCOAL lists: SNPHAP lists: SNPHARVESTER lists: SNP-HWE lists: TAGSNP lists: FASTMAP (2) lists: FASTSLINK lists: GASP lists: GENOGRAM-MAKER lists: GENEHUNTER++SAD lists: GENEPI.JAR lists: BDGEN lists: TLINKAGE lists: GENOME lists: EASYPOP lists: GENOMESIMLA lists: TRAP lists: CARTHAGENE lists: ACT lists: ADMIXMAP lists: 2DMAP lists: ALBERT lists: 2SNP lists: AGEINF lists: ALLASS lists: PEDIGREEQUERY lists: PATH lists: MULTIQTL lists: SPERMSEG lists: FASTER lists: Platypus lists: KIN lists: SNP ASSISTANT lists: GRONLOD lists: COMBIN lists: ARLEQUIN lists: SEGPATH lists: JENTI lists: SCOUT lists: HAPLOREC lists: UNPHASED lists: POWER lists: HAPLO 1 lists: HAPLO 2 lists: CHIP2SPELL lists: MAP MANAGER QTX lists: G-MENDEL lists: ASSOCIATIONVIEWER lists: WHICHRUN lists: GENECLASS lists: MAREYMAP lists: HELIXTREE lists: SVCC lists: GENEHUNTER-MODSCORE lists: FAMHAP lists: BAMA lists: WEBQTL lists: HAPLOVISUAL lists: CASPAR lists: GC/GCF lists: MIXSCORE lists: POWQ lists: QTLNetwork lists: SIMULAPLOT lists: SQTDT/SPDT lists: FESTA lists: BOTTLENECK lists: PAP lists: QUANTO lists: R/QTL lists: SNPEM lists: GENEPOOL lists: EPISTACY lists: VITESSE lists: LEA lists: DMAP lists: MOSCPHASER lists: UMAKE lists: TDT-AE lists: HAPLOWSER lists: STEPC lists: RECORD lists: QUTIE lists: R/COMPOSITELD lists: FINESSE lists: R/EHP lists: R/HCLUST lists: STEPWISE lists: genehunter-imprinting lists: PBAT lists: R/BARS lists: HARDY lists: R/ARP.GEE lists: R/COVIBD lists: STRAT lists: TREELD lists: TUNA lists: SIBSIM lists: IGG lists: ALLELIX lists: ALLEGRO lists: ALOHOMORA lists: ALP lists: AMELIA lists: ANALYZE lists: ANCESTRY lists: APE lists: BARS lists: APL-OSA lists: APM lists: ARIEL lists: GENOMIZER lists: ASP/ASPSHARE lists: BIMBAM lists: BIOIDE lists: BIOLAD-DB lists: BLADE lists: BLOCK lists: BOOLD lists: BOOSTRAPPER lists: BPPH lists: BQTL lists: DNABASER lists: Calculator for Association with Two Stage design lists: CC-QLS lists: CCRAVAT lists: CCREL lists: CEPH2CRI lists: CEPH2MAP lists: EVOKER lists: CFC lists: CHECKHET lists: MATLINK lists: CHECKMATRIX lists: CHIAMO lists: CHROMOSCAN lists: CHROMOSEG lists: COPE lists: HCLUST lists: COVIBD lists: CRIMAP-PVM lists: CROSSFIND lists: DGENE lists: EHPLUS lists: DHSMAP lists: DISENTANGLER lists: MAKEPED lists: DOLINK lists: DPPH lists: GREGOR lists: EAGLET lists: EASYLINKAGE/EASYLINKAGE-PLUS lists: EH lists: EHAP lists: EHP lists: EMLD lists: EPDT lists: ERPA lists: EXOMEPICKS lists: R/META lists: FASTEHPLUS lists: FASTLINK lists: FBAT lists: FINETTI lists: FIRSTORD lists: FISHER lists: GAIA lists: GAP lists: GAS lists: GCHAP lists: GDA lists: GEMS lists: GENECOUNTING lists: GENEFINDER lists: GENEHUNTER lists: GENEHUNTER-IMPRINTING lists: GENEHUNTER-PLUS lists: GENEPOP lists: GENERECON lists: GENESPRING GT lists: GENIE lists: GENETIC POWER CALCULATOR lists: GENETSIM lists: GENOOM lists: GENEVAR lists: GENEWEAVER lists: GENOCHECK lists: GENOPROOF lists: GENTOOLS lists: GEST lists: GEVALT lists: GGT lists: GHOST lists: GLIDERS lists: GLUE lists: GMA lists: GMCHECK lists: GSMA lists: GTOOL lists: GWAPOWER lists: HAP 2 lists: HAPAR lists: HAPASSOC lists: HAPBLOCK lists: HAPGEN lists: HAPINFERX lists: HAPLOBLOCK lists: HAPLOBUILD lists: HAPLOPOOL lists: HAPLORE lists: HAPLO.STAT lists: HAPLOT lists: HAPLOTTER lists: TWOLOC lists: HAPLOTYPE ESTIMATION lists: HAPLOTYPER lists: HAPMINER lists: HAP-SAMPLE lists: HAPSIMU lists: HIT lists: HOMOG/HOMOGM lists: HOTSPOTTER lists: HPLUS lists: HS-TDT lists: HTR lists: HTSNPER lists: MDR-PDT lists: INTERSNP lists: IMPUTE lists: NOPAR lists: JLIN lists: JOINMAP lists: JPSGCS lists: J/QTL lists: KING lists: LAMARC lists: LINKAGE-IMPRINT lists: LINKBASE lists: LIPED lists: LNKTOCRI lists: LOCUSZOOM lists: LOGINSERM ESTIHAPLO lists: LOH-LINKAGE lists: LOKI lists: LOT lists: L-POP lists: LRP lists: LRTAE lists: LTSOFT lists: MADMAPPER lists: Marker And Gene Interpolation and Correlation lists: MALDSOFT lists: MAMA lists: MANTEL-STRUCT lists: MAP/MAP+/MAP+H/MAP2000 lists: MAPCHART lists: MIDAS lists: MAPDISTO lists: MAPDRAW lists: MAPINSPECT lists: MAPL lists: MARGARITA lists: MDBLOCKS lists: MAPMAKER/EXP lists: MAPMAKER/HOMOZ lists: MAPMAKER/QTL lists: MAPQTL lists: MCQTL lists: MEGA2 lists: MEGASNPHUNTER lists: MENDEL lists: MERLIN lists: MFLINK lists: MINIMAC lists: MINSAGE lists: MITPENE lists: MKGST lists: MMDRAWER lists: MLBGH lists: MLD lists: MLR-TAGGING lists: PEDMANAGER lists: SAGE lists: MPDA lists: MULTIDISEQ lists: MULTIMAPPER lists: MULTIMAPPER/OUTBRED lists: MULTIPOPTAGSELECT lists: MULTISIM lists: MUTAGENESYS lists: NOCOM lists: NUCULAR lists: ONEMAP lists: OSIRIS lists: P ACT lists: PASS PEDIGREE lists: PAWE lists: PDA lists: PDPSYS lists: PDT lists: PED lists: PEDAGREE lists: PEDCHECK lists: PEDSTATS lists: PEDSYS lists: PEDVIZAPI lists: PEER lists: PHASE lists: PLABSIM lists: PL-EM lists: POINTER lists: POOL STR lists: POWERMARKER lists: POWERTRIM lists: POWTEST lists: PREPLINK lists: PREST lists: PROBMAX lists: PROC QTL lists: PROFILER lists: PRT lists: PSAT lists: SAS/GENETICS lists: PSEUDO lists: PSEUDOMARKER lists: PSEUDOMARKER.M lists: R/LDHEATMAP lists: QTL-ALL lists: QTL Cartographer lists: QTL EXPRESS lists: QU-GENE lists: RISCALW lists: RC-TDT lists: REAPER lists: RELATIVE lists: RELATIVEFINDER lists: RELCHECK lists: RELPAIR lists: RELTYPE lists: RHMAP lists: ROMPREV lists: ROSATTA SYLLEGO SYSTEM lists: R/GAP lists: R/HAPASSOC lists: R/IBDREG lists: R/LAPSTRUCT lists: R/LDGROUP lists: R/LUCA lists: R/METASIM lists: R/ONEMAP lists: R/PIAGE lists: R/POOLSCORE lists: R/POPGEN lists: R/QTLBIM lists: R/SNP.PLOTTER lists: SDMINP lists: SELSIM lists: SEQUENCE LD/SEQUENCE LDHOT lists: SIBERROR lists: SIBLINK lists: SIB-PAIR lists: SILCLOD lists: SIMLA lists: SNP CHART lists: SIMLINK lists: SIMPED lists: SIMPLE lists: SIMULA lists: SIMULATE lists: SIMUPOP lists: SIMWALK lists: START lists: SKAT lists: SLINK lists: SMOOTH lists: Suite of Nucleotide Analysis Programs lists: SNAP 3 lists: SNPALYZE lists: SNPFILE lists: SNPLINK lists: SNPP lists: SNP.PLOTTER lists: SNPTEST lists: SPAM lists: SPECTRAL-GEM lists: SPERM lists: SPIP lists: SPLAT lists: TAGSTER lists: SPLINK lists: SSAHASNP lists: SUMSTAT lists: SUP lists: SWEEP lists: TAGGER lists: TFPGA lists: TREESELECT lists: UNKNOWN lists: UTIL lists: WHAIT lists: ZAPLO lists: HAPBLOCK 2 lists: PLABQTL lists: TASSEL lists: MCLEEPS lists: SASGENE lists: PANGAEA lists: TOMCAT lists: SCORE-SEQ lists: SASQUANT lists: QMSIM lists: PIAGE lists: PEDPACK lists: INSEGT lists: IBDREG lists: GLFSINGLE/GLFTRIO/GLFMULTIPLES lists: GGSD lists: ECLIPSE lists: CHROMSCAN lists: COMPOSITELD lists: BOOST lists: ARP.GEE lists: BOREL lists: GASSOC lists: MENDELSOFT lists: PLINK/SEQ lists: POLYPHEN lists: SPREG lists: MOLKIN lists: PRESTO: Genetic Association Analysis Software lists: ENDOG lists: BEAGLECALL lists: GWASELECT lists: HEGESMA lists: SNIPPEEP lists: TAGIMPUTE lists: SNPMSTAT lists: SNP HITLINK lists: MECPM lists: R/FEST lists: MAOS lists: SUPERLINK lists: PEDFIDDLER lists: VG lists: HAPSTAT lists: QTDT lists: GRIDQTL lists: VH lists: R/QTLDESIGN lists: PyPop lists: ANTMAP lists: MDR lists: WEIGHTED FDR lists: THESIAS lists: DMLE lists: SGS lists: BAYESFST lists: HWMET lists: GRR lists: AUTOSCAN lists: TRIMHAP lists: ILLUMINUS lists: PELICAN lists: HAPLOPAINTER lists: HOMOZYGOSITYMAPPER lists: GERMLINE lists: PLINK lists: MACH 1.0 lists: BEAGLE lists: BIRDSUITE lists: BREAKDANCER lists: CAROL lists: CASAVA lists: CYRILLIC lists: DINDEL lists: GenABEL lists: GATK lists: PEDIGRAPH lists: MADELINE lists: METAL lists: OLORIN lists: PEDHUNTER lists: POLYMUTT lists: SAMTOOLS lists: SNAP - SNP Annotation and Proxy Search lists: STRUCTURE lists: SVA lists: SYZYGY lists: VAAST lists: Hapmix lists: Ancestrymap lists: Hmmer lists: PROGENY lists: VarScan lists: MORGAN lists: CMAP lists: SIMHAP lists: SIFT lists: ANNOVAR lists: Body Mass Index Calculator lists: PolyPhen: Polymorphism Phenotyping has parent organization: Feinstein Institute for Medical Research has parent organization: Iowa State University; Iowa; USA			THIS RESOURCE IS NO LONGER IN SERVICE	nif-0000-33506	http://lab.rockefeller.edu/ott/geneticsoftware	http://linkage.rockefeller.edu/soft/	SCR_013155	An Alphabetic List of Genetic Analysis Software	2026-09-12 12:57:59	9

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