OBIToolsSet of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.https://git.metabarcoding.org/obitools/obitools/wikis/homeobitoolsbiotools:obitoolsCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacPythonhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/obitools-scripts-and-library-for-sequence-analysis.htmlSoftware cataloguehttp://metabarcoding.org//obitools/doc/welcome.html#installing-the-obitoolsGeneral10.1111/1755-0998.1242825959493Eric Coissaceric.coissac@inria.frhttp://metabarcoding.org/obitoolsPersonPrimary contactDeepConsensusDeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.https://github.com/google/deepconsensusdeepconsensusbiotools:deepconsensus1.2.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxPythonBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0850Sequence setdeepconsensus run --subreads_to_ccs=shard_id.subreads_to_ccs.bam --ccs_bam=shard_id.ccs.bam --checkpoint=model/checkpoint --output=shard_id.output.fastq10.1038/s41587-022-01435-736050551screen_assemblyScreen a bacterial assembly (contigs/CDS or proteins) for nucleotide or protein sequences.
Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. Generates multiple CSVs and plots that describe which genes are present and how variable their sequence is. Can use DNA or protein query sequences (GOIs) and DNA contigs/fastas or protein fastas as database (db) to search in.https://github.com/shimbalama/screen_assemblyscreen_assemblybiotools:screen_assemblyv1ScriptCommand-line toolhttp://edamontology.org/topic_0196Sequence assemblyPythonMITMaturehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttps://github.com/shimbalama/screen_assemblyRepositoryhttps://github.com/shimbalama/screen_assembly/wikiGeneral10.1038/s41588-019-0417-831133745PMC6650292PrimaryMark R. Davieshttps://orcid.org/0000-0001-6141-5179PersonNuclearPhaserNuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.https://github.com/JanaSperschneider/NuclearPhasernuclearphaserbiotools:nuclearphaser1.1Scripthttp://edamontology.org/topic_0622GenomicsLinuxMacPythonGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttps://github.com/JanaSperschneider/NuclearPhaserRepositoryhttps://github.com/JanaSperschneider/NuclearPhaser/blob/main/README.mdQuick start guideJana Sperschneiderhttps://github.com/JanaSperschneiderseqlibseqlib is a type-safe Rust library for working with DNA and RNA sequences.https://github.com/selkamand/seqlibseqlibbiotools:seqlibLibraryhttp://edamontology.org/topic_3321Molecular geneticshttp://edamontology.org/topic_0622GenomicsMacWindowsLinuxRustNot licensedMaturehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2977Nucleic acid sequencehttps://github.com/selkamand/seqlibRepositoryhttps://github.com/selkamand/seqlib/blob/main/README.mdAPI documentationsalmonKallistoMtxTo10xKallisto and Alevin (and possibly other tools) output an MTX file and associated labels that are not consistent with the old-style 10X, meaning that routines designed to parse those files cannot be used. This tool transforms (in the mathematical sense) the matrix, and reformats the genes file (essentially duplicating the column) to match those earlier conventions.https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiarysalmonkallistomtxto10xbiotools:salmonkallistomtxto10x0.0.1+galaxy6Command-line toolhttp://edamontology.org/topic_4028Single-cell sequencingPythonMITFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3916MTXhttps://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/Repository10.1101/2020.04.08.032698PrimarySouth Green Genome HubsThe South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).https://banana-genome-hub.southgreen.fr/South_Green_Genome_Hubsbiotools:South_Green_Genome_HubsDatabase portalhttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0621Model organismsJavaScriptPHPGPL-2.0Genome HubMatureFree of chargeDataToolsFrancehttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_1929FASTAhttps://github.com/SouthGreenPlatform/genomehubsIssue trackerhttps://banana-genome-hub.southgreen.fr/content/term-serviceTerms of usetripalusesbanana_genome_hubincludescoffee_genome_hubincludescocoa_genome_hubincludesrice_genome_hubincludessugarcane_genome_hubincludessouthgreenincludedIn10.1093/database/bat03523707967PMC3662865Primary10.1093/nar/gku110825392413PMC4383925Primary10.1093/hr/uhac22136479579PMC9720444Primary10.1016/j.xplc.2022.10033035617961PMC9482989UsageGaetan Drocdroc@cirad.frhttps://orcid.org/0000-0003-1849-1269PersonPrimary contactDeveloperDocumentorProviderSupportAlexis Dereeperalexis.dereeper@ird.frMathieu Rouardm.rouard@cgiar.orghttps://orcid.org/0000-0003-1849-1269Primary contactMaintainerSupportValentin Guignonv.guignon@cgiar.orgChrisitine Tranchantchristine.tranchant@ird.frStéphanie Bocsstephanie.sidibe-bocs@cirad.frfastplongUltrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).https://github.com/OpenGene/fastplongfastplongbiotools:fastplongCommand-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0080Sequence analysisMITFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3218Sequencing quality controlhttps://github.com/OpenGene/fastplongRepositoryhttps://github.com/OpenGene/fastplong/issuesIssue tracker10.1002/imt2.10738868435PMC10989850MethodMentioned as Citation in the git repository.
Publication describes only the (short read) tool fastp.OpenGenehttps://github.com/OpenGeneOpenGene - Open Source Genomics Toolbox
Open source tools for NGS data analysisNanoPackVisualizing and processing long-read sequencing data.https://github.com/wdecoster/nanopacknanopackbiotools:nanopack1.1.0Command-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxMacPythonVIBhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0564Sequence visualisationhttps://github.com/wdecoster/nanopackGeneralnanoplotincludes10.1093/bioinformatics/bty14929547981PMC6061794Wouter De Costerwouter.decoster@molgen.vib-ua.bePersonPrimary contacthmmsim (genouest)Collect profile HMM score distributions on random sequences.http://webservices.genouest.org/opal2/dashboard?command=docshmmsim_genouestbiotools:hmmsim_genouest1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2734Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773ReviewBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmsearch (genouest)Search profile(s) against a sequence database.http://webservices.genouest.org/opal2/dashboard?command=docshmmsearch_genouestbiotools:hmmsearch_genouest1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2733Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773ReviewBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmscan (genouest)Search sequence(s) against a profile database.http://webservices.genouest.org/opal2/dashboard?command=docshmmscan_genouestbiotools:hmmscan_genouest1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2732Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmfetch (genouest)Retrieve profile HMM(s) from a file.http://webservices.genouest.org/opal2/dashboard?command=docshmmfetch_genouestbiotools:hmmfetch_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2731Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmemit (genouest)Sample sequence(s) from a profile HMM.http://webservices.genouest.org/opal2/dashboard?command=docshmmemitbiotools:hmmemit1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2730Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmconvert (genouest)Convert between profile HMM file formats.http://webservices.genouest.org/opal2/dashboard?command=docshmmconvert_genouestbiotools:hmmconvert_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2729Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1006/jmbi.1994.11048107089OtherBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmalign (genouest)Align sequences to a profile HMM.http://webservices.genouest.org/opal2/dashboard?command=docshmmalign_genouestbiotools:hmmalign_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2727Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contactProteoMirExpressWeb server that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks.http://jjwanglab.org/proteomirexpress/proteomirexpressbiotools:proteomirexpressWeb applicationhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2497Pathway or network analysishttp://www.mybiosoftware.com/proteomirexpress-inferring-microrna-and-protein-centered-regulatory-networks.htmlSoftware cataloguehttp://jjwanglab.org/proteomirexpress/helpGeneral10.1074/mcp.o112.01985123924514PMC3820948http://jjwanglab.org/proteomirexpress/aboutPersonPrimary contactPOPDISTNewly-developed population genetic data analysis program. It calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures.http://genetics.agrsci.dk/~bernt/popgen/popdistbiotools:popdistCommand-line toolhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3056Population geneticsLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3478Phylogenetic tree reconstructionhttp://www.mybiosoftware.com/popdist-1-2-3-population-genetic-data-analysis-program.htmlSoftware cataloguehttp://genetics.agrsci.dk/~bernt/popgen/#docGeneral10.1111/j.1755-0998.2009.02623.x21564908http://pure.au.dk/portal/en/persons/id(782adba8-3ec8-409b-afd7-81f2d75579b2).htmlPersonPrimary contactH-VDWNovel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence.http://www.cbi.seu.edu.cn/H-VDW/H-VDW.htmh-vdwbiotools:h-vdwWeb applicationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0272Residue interaction predictionhttp://www.mybiosoftware.com/h-vdw-predicting-hydrogen-bonds-or-van-der-waals-contacts-in-protein-nucleic-acid-complexes.htmlSoftware cataloguehttp://www.cbi.seu.edu.cn/H-VDW/manual.htmUser manual10.1016/j.jmgm.2011.08.00121920789jansen.woo.seu@gmail.comhttp://www.cbi.seu.edu.cn/cbi/PersonPrimary contactImpG-SummarySoftware package implementing methods for imputation from summary statistics and accompanying data. The software takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis. It outputs summary association statistics at all 1000 Genomes variants.http://bogdan.bioinformatics.ucla.edu/software/impg/impg-summarybiotools:impg-summaryCommand-line toolhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_2885DNA polymorphismLinuxhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2238Statistical calculationhttp://www.mybiosoftware.com/impg-summary-1-0-1-imputation-summary-statistics.htmlSoftware cataloguehttp://bogdan.bioinformatics.ucla.edu/wp-content/uploads/sites/3/2013/07/ImpG_v1.0_User_Manual_31July13.pdfUser manual10.1093/bioinformatics/btu41624990607PMC4184260pasaniuc@ucla.eduhttp://bogdan.bioinformatics.ucla.edu/contact/PersonPrimary contactPOPTREEProgram for making population trees from allele frequency data.http://www.kms.ac.jp/~genomelb/takezaki/poptree2/index.htmlpoptreebiotools:poptreeDesktop applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_2269Statistics and probabilityWindowshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2238Statistical calculationhttp://www.mybiosoftware.com/poptree-2-population-trees-allele-frequency-data.htmlSoftware cataloguehttp://www.kms.ac.jp/~genomelb/takezaki/poptree2/userguide.pdfGeneral10.1093/molbev/msu09324603277takezaki@med.kagawa-u.ac.jpPersonPrimary contactBioPigFramework for genomic data analysis using Apache Pig and Hadoop.https://sites.google.com/a/lbl.gov/biopig/biopigbiotools:biopigCommand-line toolhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0654DNALinuxMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/biopig-hadoop-based-analytic-toolkit-for-large-scale-sequence-data.htmlSoftware cataloguehttps://sites.google.com/a/lbl.gov/biopig/General10.1093/bioinformatics/btt52824021384Zhong Wangzhongwang@lbl.govhttp://jgi.doe.gov/our-science/scientists-jgi/genome-analysis/PersonPrimary contactSMRT AnalysisAbioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences.http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/smrt_analysisbiotools:smrt_analysisCommand-line toolSuiteDesktop applicationhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/smrt-analysis-2-0-1-software-suite-sequence-alignment-assembly-variant-detection-base-modification-discovery.htmlSoftware cataloguehttp://www.pacb.com/support/software-downloads/General10.1186/2041-9414-2-1022185597PMC3264494http://www.pacb.com/contact-us/PersonPrimary contactMGIPSuite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.http://mgip.biology.gatech.edumgipbiotools:mgipWeb applicationSuitehttp://edamontology.org/topic_0605Informaticshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168SequencingLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3227Variant callinghttp://www.mybiosoftware.com/mgip-meningococcus-genome-informatics-platform.htmlSoftware cataloguehttp://mgip.biology.gatech.edu/ODfaq/General10.1093/nar/gkp28819468047PMC2703879Lee S. Katzlskatz@gatech.eduhttp://mgip.biology.gatech.edu/contact.phpPersonPrimary contactCOUGERFramework for identifying co-factors associated with uniquely-bound genomic regions.http://couger.oit.duke.educougerbiotools:cougerCommand-line toolWeb applicationhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3307Computational biologyLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/couger-1-2-0-identifying-co-factors-uniquely-bound-genomic-regions.htmlSoftware cataloguehttp://couger.oit.duke.edu/documentation/General10.1093/nar/gku43524861628PMC408613910.1007/978-3-642-37195-0_1210.1093/nar/gku43524861628PMC4086139Couger Supportcouger@info.uaic.roPersonPrimary contactRALUCA GORDÂNraluca.gordan@duke.eduhttp://www.genome.duke.edu/labs/gordan/index.phpPersonPrimary contactIPGWASIntegrated pipeline for rational quality control and association analysis of genome-wide genetic studies.http://sourceforge.net/projects/ipgwas/ipgwasbiotools:ipgwasDesktop applicationhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3517GWAS studyLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/ipgwas-3-4-integrated-pipeline-for-genome-wide-association-studies.htmlSoftware cataloguehttps://sourceforge.net/projects/ipgwas/General10.1016/j.bbrc.2012.04.11722564732Yan-HuiFannolanfyh@gmail.comhttp://sourceforge.net/projects/ipgwas/PersonPrimary contactYou-QiangSongsongy@hkucc.hku.hkPersonPrimary contactPathoscopeTakes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.http://sourceforge.net/projects/pathoscope/pathoscopebiotools:pathoscopeCommand-line toolhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_2269Statistics and probabilityLinuxhttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/pathoscope-0-1-ngs-reads-mixture-sample-multiple-strains-genomes.htmlSoftware cataloguehttps://sourceforge.net/projects/pathoscope/files/pathoscope2.0_v0.02_tutorial.pdf/downloadUser manual10.1186/2049-2618-2-3325225611PMC4164323Changjin Hongcjhong@bu.eduhttp://jlab.bu.eduPersonPrimary contactWilliam Evan Johnsonwej@bu.eduPersonPrimary contactSeqCalcThis tool assists the research personnel in computational sequence analysis and automated experimental calculations.https://code.google.com/p/seqcalc/seqcalcbiotools:seqcalcDesktop applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0077Nucleic acidsWindowshttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/seqcalc-1-0-portable-software-sequence-analysis.htmlSoftware cataloguehttps://code.google.com/archive/p/seqcalc/General10.6026/9732063000508521364786PMC3041003yplim@cnu.ac.krhttps://sites.google.com/site/vigneshdhandapani/PersonPrimary contactNSITEPrograms that perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.http://www.softberry.com/freedownloadhelp/nsite/description.htmlnsitebiotools:nsiteCommand-line toolhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsLinuxMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/nsite-studying-tran-scription-regulatory-elements.htmlSoftware cataloguehttp://www.softberry.com/freedownloadhelp/nsite/description.htmlGeneral10.1093/bioinformatics/btv40426142184PMC4612222Solovyev VVsolovictor@gmail.comhttp://www.molquest.kaust.edu.sa/PersonPrimary contactNPSInteractive Web server dedicated to protein sequence analysis and available for the biologist community.http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.htmlnps-proteinbiotools:nps-proteinWeb servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/nps-20131114-interactive-web-server-dedicated-protein-sequence-analysis.htmlSoftware cataloguehttps://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.htmlGeneral10.1016/s0968-0004(99)01540-610694887Gilbert DELEAGEgilbert.deleage@ibcp.frhttp://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_who.htmlPersonPrimary contactRaphael TERREUXraphael.terreux@ibcp.frhttps://prabi.ibcp.fr/htm/site/web/contact/PersonPrimary contactSULDEXThe packages is designed to use high throughput sequencing to simultaneously analyze binding dissociation constants for large repertoires of sequences.http://www.evolutionarygenomics.com/ProgramsData/SULDEX/SULDEX.htmlsuldexbiotools:suldexCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0749Transcription factors and regulatory sitesLinuxMachttp://edamontology.org/operation_2403Sequence analysisBinding dissociation constant analysishttp://www.mybiosoftware.com/suldex-0-01-simultaneous-ultra-high-throughput-ligand-dissociation-experiment.htmlSoftware cataloguehttp://www.evolutionarygenomics.com/ProgramsData/SULDEX/Usage.txtUser manual10.1371/journal.pone.002610522069446PMC3206046David.Pollock@UCDenver.eduhttp://www.evolutionarygenomics.com/contact.htmlPersonPrimary contactiTagPlotTool to accurately compute and interactively visualize tag density (read coverage)from genomic sequencing data.http://sourceforge.net/projects/itagplot/itagplotbiotools:itagplotDesktop applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622GenomicsLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/itagplot-1-0-computation-and-interactive-visualization-of-tag-density.htmlSoftware cataloguehttps://sourceforge.net/projects/itagplot/General10.1093/bioinformatics/btv16625792550PMC4495303Jeong-Hyeon Choijechoi@gru.eduhttp://sourceforge.net/projects/itagplot/PersonPrimary contactNUCGENReads wedge (or local doublet) and basepair parameters calculates local helical parameters from local doublet parameters, then applies the base-pair and helical parameters to succesive basepairs after transforming the already generated ones to bring the topmost one in the (x-y) plane.http://nucleix.mbu.iisc.ernet.in/nucgen/index.htmnucgenbiotools:nucgenWeb applicationhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/nucgen-generation-analysis-sequence-dependent-nucleic-acid-structures.htmlSoftware cataloguehttp://nucleix.mbu.iisc.ernet.in/nucgen/news.htmGeneral10.1093/bioinformatics/11.3.2817583696mb@mbu.iisc.ernet.inhttp://nucleix.mbu.iisc.ernet.in/index.htmPersonPrimary contactdiffRepsThis software is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. It takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.https://github.com/shenlab-sinai/diffrepsdiffrepsbiotools:diffrepsCommand-line toolScripthttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_3277Sample collectionsLinuxPerlGPL-3.0Maturehttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/diffreps-1-55-1-finding-differential-chromatin-modification-sites-chip-seq-data.htmlSoftware cataloguehttps://github.com/shenlab-sinai/diffrepsGeneral10.1371/journal.pone.006559823762400PMC3677880Dr. Li Shenli.shen@mssm.eduhttp://neuroscience.mssm.edu/shen/PersonPrimary contactbiojs-alg-seqregionObject and function to deal with a sequence region (reg:start-end).https://github.com/homonecloco/biojs-alg-seqregionbiojs-alg-seqregionbiotools:biojs-alg-seqregion0.1.1Libraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacJavaScripthttp://edamontology.org/operation_2403Sequence analysishttps://github.com/homonecloco/biojs-alg-seqregionGeneral10.7554/elife.0700926153621PMC4495654BioJSInstituteProviderRicardo H. Ramirez-Gonzalezricardo.ramirez-gonzalez@tgac.ac.ukPersonPrimary contactsecureSeqA suite of secure sequencing analysis tools.http://www.hcbravo.org/projects/secureseq/secureseqbiotools:secureseqCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0080Sequence analysisLinuxShellhttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/secureseq-secure-sequencing-analysis-tools.htmlSoftware cataloguehttp://www.hcbravo.org/projects/secureseq/General10.1093/bioinformatics/btw07326873931PMC4908319hcorrada@gmail.comhttp://www.hcbravo.org/PersonPrimary contactNOVAProgram designed to analysis complexome profiling data.http://www.bioinformatik.uni-frankfurt.de/tools/nova/index.phpnovabiotools:novaDesktop applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksWindowsJavahttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2409Data handlinghttp://www.mybiosoftware.com/nova-visualization-and-analysis-of-complexome-profiling-data.htmlSoftware cataloguehttp://www.bioinformatik.uni-frankfurt.de/tools/nova/index.phpGeneralhttp://www.bioinformatik.uni-frankfurt.de/tools/nova/index.php?go=tutorialsUser manual10.1093/bioinformatics/btu62325301849Ina Kochina.koch@bioinformatik.uni-frankfurt.dehttp://www.bioinformatik.uni-frankfurt.de/tools/nova/index.php?go=contactPersonPrimary contactHeiko Gieseh.giese@bioinformatik.uni-frankfurt.dehttp://www.bioinformatik.uni-frankfurt.de/tools/nova/index.php?go=contactPersonPrimary contactGenomizerPlatform independent Java program for the analysis of genome wide association experiments. The software implements the workflow of an association experiment, including data management, single-point and haplotype analysis, “lead” definition, and data visualization.http://www.ikmb.uni-kiel.de/resources/download-tools/software/genomizergenomizerbiotools:genomizerDesktop applicationhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3517GWAS studyLinuxWindowsJavahttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3208Genome visualisationhttp://www.mybiosoftware.com/genomizer-1-2-0-analysis-genome-wide-association-experiments.htmlSoftware cataloguehttp://www.ikmb.uni-kiel.de/resources/download-tools/software/genomizerGeneral10.1002/humu.2030616652332sekretariat@mucosa.dePersonPrimary contactSePIAComprehensive RNA Sequencing workflow for standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.http://anduril.org/sepia/sepiabiotools:sepiaCommand-line toolhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysisLinuxChttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/sepia-rna-sequence-processing-integration-and-analysis.htmlSoftware cataloguehttp://anduril.org/sepia/doc.htmlGeneral10.1186/s13040-016-0099-z27213017PMC4875694https://groups.google.com/forum/?fromgroups#!forum/anduril-devPersonPrimary contactVarioBoxDesktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence metadata is obtained from Locus Reference Genomic (LRG) and RefSeq databases.http://bioinformatics.ua.pt/software/variobox/varioboxbiotools:varioboxDesktop applicationhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacJavahttp://edamontology.org/operation_2451Sequence comparisonhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0361Sequence annotationhttp://www.mybiosoftware.com/variobox-1-4-4-exploring-human-genetic-variations.htmlSoftware cataloguehttp://bioinformatics.ua.pt/software/variobox/General10.1002/humu.2247424186831jlo@ua.pthttp://bioinformatics.ua.pt/PersonPrimary contactSambambaThis tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.http://www.open-bio.org/wiki/Sambambasambambabiotools:sambambaCommand-line toolhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3170RNA-SeqLinuxMacDhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://www.mybiosoftware.com/sambamba-0-5-1-tools-for-working-with-sambam-data.htmlSoftware cataloguehttps://github.com/lomereiter/sambambaGeneralhttps://lomereiter.github.io/sambamba/docs/sambamba-view.htmlUser manual10.1093/bioinformatics/btv09825697820PMC4765878http://lomereiter.github.io/PersonPrimary contactPCICalculates the barcode gap probability of correct identification (PCI) of species.http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=17pcibiotools:pciCommand-line toolhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_0610EcologyLinuxWindowsMacPerlhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3221Species frequency estimationhttp://www.mybiosoftware.com/pci-1-0-calculate-barcode-gap-probability-correct-identification-species.htmlSoftware cataloguehttps://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/barcode_pci/pci.htmlGeneral10.1371/journal.pone.005452923390499PMC3563529John L. Spougespouge@ncbi.nlm.nih.govhttp://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/index/group.htmlPersonPrimary contacttaxator-tkAlgorithm and the accompanying software, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.https://github.com/fungs/taxator-tktaxator-tkbiotools:taxator-tkSuitehttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_0080Sequence analysisLinuxC++http://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3460Taxonomic classificationhttp://www.mybiosoftware.com/taxator-tk-1-2-1-taxonomic-sequence-assignment.htmlSoftware cataloguehttps://github.com/fungs/taxator-tk/blob/master/INSTALL.mdGeneralInstall guidehttps://github.com/fungs/taxator-tk/blob/master/USAGE.mdUser manual10.1093/bioinformatics/btu74525388150PMC4380030Johannes Droegejohannes.droege@uni-duesseldorf.dePersonPrimary contactParTIESDesigned for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.https://github.com/oarnaiz/ParTIESpartiesbiotools:partiesCommand-line toolhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0654DNALinuxWindowsMacRPerlhttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/parties-paramecium-toolbox-for-interspersed-dna-elimination-studies.htmlSoftware cataloguehttps://github.com/oarnaiz/ParTIES/blob/master/user_manual.pdfUser manual10.1093/bioinformatics/btv69126589276Linda Sperlinglinda.sperling@i2bc.paris-saclay.frhttps://github.com/oarnaizPersonPrimary contactGenePaletteGenome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.http://www.genepalette.orggenepalettebiotools:genepaletteDesktop applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0654DNALinuxWindowsMacJavahttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://www.mybiosoftware.com/genepalette-2-0-genome-sequence-visualization-navigation.htmlSoftware cataloguehttp://www.genepalette.org/documentation.htmlGeneral10.1016/j.ydbio.2004.04.01115223345http://www.genepalette.org/contact.htmlPersonPrimary contactLmCGSTBioinformatic pipeline that takes in raw next-generation sequencing reads, calculates a subject HCC profile, compares it to an expandable database, assigns a sequence type, and performs a phylogenetic analysis.http://sourceforge.net/projects/lmcgst/?source=navbarlmcgstbiotools:lmcgstCommand-line toolhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3324Infectious diseaseLinuxPerlhttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/lmcgst-molecular-characterization-with-next-generation-sequence-data.htmlSoftware cataloguehttps://sourceforge.net/projects/lmcgst/?source=navbarGeneral10.1186/s12866-015-0526-126490433PMC4618880Arthur W. PightlingArthur.Pightling@fda.hhs.govhttp://sourceforge.net/projects/lmcgst/?source=navbarPersonPrimary contactSPADSA population genetics software computing several summary statistics from populations or groups of populations, and implementing two clustering algorithms to study the genetic structure of populations. It has been specifically developed for the analysis of DNA sequences. The first aim of SPADS is to compute, on real datasets, the summary statistics computed by PhyloGeoSim on each simulated datasets.http://ebe.ulb.ac.be/ebe/SPADS.htmlspadsbiotools:spadsDesktop applicationhttp://edamontology.org/topic_3056Population geneticshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacRJavahttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/spads-1-1-spatial-population-analysis-dna-sequences.htmlSoftware cataloguehttp://ebe.ulb.ac.be/ebe/SPADS_files/SPADS_1.0_manual_221116.pdfGeneral10.1111/1755-0998.1220024215429Simon.Dellicour@ulb.ac.behttp://ebe.ulb.ac.be/ebe/ebe-Welcome.htmlPersonPrimary contactSIMregA tool to perform maker-set association analysis. Association analysis at gene, pathway, or exon levels (here by marker-set analysis) hold great promise in evaluating modest etiological effects of genes with GWAS or sequence data.http://www4.stat.ncsu.edu/~jytzeng/software.phpsimregbiotools:simregCommand-line toolhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3517GWAS studyLinuxMacRhttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/simreg-1-32-gene-trait-similarity-regression-for-marker-set-association-analysis.htmlSoftware cataloguehttp://www4.stat.ncsu.edu/~jytzeng/software_simreg.phpGeneral10.1016/j.ajhg.2011.07.00721835306PMC3155192jytzeng@stat.ncsu.eduhttp://www4.stat.ncsu.edu/~jytzeng/PersonPrimary contactNUPARM-PlusProgram for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices.http://nucleix.mbu.iisc.ernet.in/nuparm/nuparm-plusbiotools:nuparm-plusCommand-line toolhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavahttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/nuparm-analysis-sequence-dependent-variations-nucleic-acid-double-helices.htmlSoftware cataloguehttp://nucleix.mbu.iisc.ernet.in/nuparm/help.htmlGeneral10.1093/bioinformatics/11.3.2817583696mb@mbu.iisc.ernet.inhttp://nucleix.mbu.iisc.ernet.in/index.htmPersonPrimary contactGenome-wide EvaluationGenome-wide evaluation under a multiple variance component model by using the maximum likelihood (ML) method and the MCMC implemented Bayesian method.http://statgen.ucr.edu/software.htmlgenome-wide_evaluationbiotools:genome-wide_evaluationCommand-line toolhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0080Sequence analysisWindowsRhttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/genome-wide-evaluation-performs-genome-wide-evaluation.htmlSoftware cataloguehttp://statgen.ucr.edu/software.htmlGeneral10.1007/s10709-010-9497-120835884PMC2948655someone@ucr.eduPersonPrimary contact