nalloNallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly,
and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional
consequences.https://github.com/genomic-medicine-sweden/nallonallobiotools:nallo0.12.0http://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3295EpigeneticsGroovyJavaMITFree of chargehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2545FASTQ-like formathttps://github.com/genomic-medicine-sweden/nalloRepositoryhttps://genomic-medicine-sweden.github.io/nallo/latest/User manual10.1093/BIOINFORMATICS/BTAG08641712762PMC12988770Lars Feuklars.feuk@igp.uu.sehttps://orcid.org/0000-0003-2355-2919PersonSPALNGenome mapping and spliced alignment of cDNA or amino acid sequenceshttps://github.com/ogotoh/spalnspalnbiotools:spalnver.3.0.8bCommand-line toolhttp://edamontology.org/topic_0102MappingCPerlC++GPL-2.0Maturehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1234Sequence set (nucleic acid)https://github.com/ogotoh/spalnRepositoryhttps://github.com/ogotoh/spalnGeneral10.1093/nar/gkag35742134803PMC1317563310.1093/bioinformatics/btn4601872804310.1093/nar/gks70822848105PMC348821110.1093/bioinformatics/16.3.1901086901210.1093/bioinformatics/btae51739152995PMC1136180910.1007/978-1-0716-1036-7_53328988710.1093/bioinformatics/btl06716500940Osamu Gotohgotoh.osamu.67a@st.kyoto-u.ac.jphttps://orcid.org/0009-0002-6750-1945PersonVerityMapVerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.https://github.com/ablab/VerityMapVerityMapbiotools:VerityMaphttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622GenomicsCCUDAPythonC++GPL-3.0Maturehttp://edamontology.org/operation_0523Mapping assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/ablab/tandemQUAST/issuesIssue tracker10.1093/bioinformatics/btaa44032657355PMC7355294sam2intervalA Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalsam2intervalbiotools:sam2intervalScripthttp://edamontology.org/topic_0622GenomicsMacWindowsLinuxPythonMITEmergingFree of chargeOpen accessGalaxyhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAMhttps://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalRepositoryRepeatAfterMeRepeatAfterMe is a package for the extension of repetitive DNA cores. The tool automatically extends a multiple sequence alignment that may represent only a fragment of a longer repetitive sequence family.https://github.com/Dfam-consortium/RepeatAfterMerepeataftermebiotools:repeataftermev0.0.7Command-line toolhttp://edamontology.org/topic_0622GenomicsMacLinuxCCC0-1.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_30092bithttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/format_3585bed6./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bitRobert HubleyPersonDeveloperJalviewJalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.https://www.jalview.org/Jalviewbiotools:Jalview2.11.5.1Desktop applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsGPL-3.0ELIXIR-UKMatureFree of chargeOpen accessToolsInteroperabilityUKhttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_1938GFF2-seqhttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3311RNAMLhttp://edamontology.org/format_1915Formathttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1939GFF3-seqhttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_1476PDBOther Input formats:
AMSA (.amsa);
JnetFile (.concise, .jnet);
PFAM (.pfam);
Substitution matrix (.matrix);
Jalview Project File (.jvp);
Jalview Feature File (.features, .jvfeatures);
Jalview Annotations File (.annotations, .jvannotations);
Predicted Aligned Error (PAE) Matrix File (.json)
...
Other Output formats:
PFAM (.pfam);
BioJS (.biojs) (interactive HTML/Javascript);
Jalview Project File (.jvp);https://discourse.jalview.org/Discussion forumhttps://issues.jalview.org/Issue trackerhttps://www.jalview.org/development/jalview_develop/OtherLatest development versionhttps://gitlab.jalview.org/jalview/jalview.gitRepositoryhttps://twitter.com/JalviewSocial mediaTwitter feedhttps://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfwSocial mediaYouTube training videoshttps://www.linkedin.com/company/104771886/Social mediahttps://www.jalview.org/downloadDownloads pagehttps://www.jalview.org/download/source/Source codehttps://www.jalview.org/download/?os=allBinariesBinaries for all platformshttps://www.jalview.org/favicon.svgIconhttps://www.jalview.org/download/other/jar/BinariesExecutable JAR filehttps://www.jalview.org/about/citationCitation instructionshttps://www.jalview.org/training/Training materialHands-on exercises, Training courses and Training videoshttps://www.jalview.org/help/faqFAQhttps://www.jalview.org/help/documentation/User manualjabawsuseschimerauseschimeraxusespymolusesbiocondaincludedIn3d-beaconsusesuniprotusespfamusesensemblusespdbusesrfamuses3d-beaconsuses10.1093/bioinformatics/btp03319151095PMC2672624Jim Procterhttp://www.lifesci.dundee.ac.uk/people/jim-procterhttps://orcid.org/0000-0002-7865-7382PersonPrimary contactGeoff Bartonhttps://www.lifesci.dundee.ac.uk/people/geoff-bartonhttps://orcid.org/0000-0002-9014-5355MuGVREThe MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. It integrates genomics tools for chromatin dynamics data.https://www.multiscalegenomics.eu/mugvrebiotools:mugvre1.0Web applicationWorkbenchhttp://edamontology.org/topic_3176DNA packaginghttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_2275Molecular modellingPHPPythonApache-2.0RIS3CAT VEISFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3210Genome indexhttp://edamontology.org/operation_0475Nucleic acid structure predictionhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2305GFFhttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_3900DNA-binding protein predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_3222Peak callinghttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAMhttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_0432Nucleosome position predictionhttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAMhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/data_3869Simulationhttp://edamontology.org/data_0883Structurehttp://vre.multiscalegenomics.euServicehttps://github.com/Multiscale-Genomics/VRERepositoryhttps://www.multiscalegenomics.eu/MuGVRE/terms-of-use/Terms of usehttp://vre.multiscalegenomics.eu/help/starting.phpQuick start guidehttps://www.multiscalegenomics.eu/MuGVRE/training/Training materialnucleosome_dynamicsincludestadbitincludesjbrowseincludesnglincludes10.1101/602474Primary1.0Laia Codólaia.codo@bsc.eshttps://orcid.org/0000-0002-6797-8746PersonPrimary contactJosep Lluís Gelpíhttp://orcid.org/0000-0002-0566-7723PersonContributorMultiscale Complex Genomics Communityvre@multiscalegenomics.euhttps://www.multiscalegenomics.eu/ConsortiumDevelopermsaDisplay multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.http://msa.biojs.netmsabiotools:msa1.0.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacJavaScriptApache-2.0Rostlab toolsBioconductorBioJSMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1984FASTA-alnVisualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF
NOTE: Actually, all these output types of data should instead be under separate "constant" operations, while the visualisation should be an unary operation, perhaps without an output.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttps://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttp://github.com/wilzbach/msaHelpdeskhttp://www.bioinf.jku.at/software/msa/Mirrorhttps://github.com/wilzbach/msaSource codehttps://cdn.bio.sh/Binarieshttps://github.com/wilzbach/msa/blob/master/LICENSETerms of usehttp://msa.biojs.netGeneral10.1093/bioinformatics/btw47427412096PMC5181560Primary10.1093/bioinformatics/btv49426315911OtherSebastian WilzbachPersonDeveloperIan SillitoeContributorGuy YachdavContributorBenedikt RauscherContributorTatyana GoldbergContributorTechnische Universität MünchenInstituteProviderGoogle Summer of Code (GSoC) 2014Funding agencyContributorBioJSInstituteProviderhttp://github.com/wilzbach/msaPersonPrimary contactUlrich Bodenhoferbodenhofer@bioinf.jku.atPersonPrimary contactCrispiA CRISPR Interactive database.http://crispi.genouest.org/crispibiotools:crispiDatabase portalhttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAA CRISPR Interactive databasehttp://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdfGeneral10.1093/bioinformatics/btp58619846435PMC2788928PrimaryGenOuestInstituteProviderGenOuest platformsupport@genouest.orghttp://www.genouest.orgPersonPrimary contactPlastParallel Local Alignment Search Tool for Database Comparison.http://www.irisa.fr/symbiose/projects/plast/plastbiotools:plast1.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCECILL-2.0MatureFree of chargehttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTASequence alignmenthttps://plast.inria.fr/General10.1186/1471-2105-10-32919821978PMC2770072PrimaryGenOuestInstituteProviderDominique Lavenierlavenier@irisa.frPersonPrimary contactCyanoLyaseManually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.http://cyanolyase.genouest.org/cyanolyasebiotools:cyanolyaseDatabase portalhttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAMotif occurence detection in protein sequenceshttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAProtein sequence alignment against known family membershttp://cyanolyase.genouest.org/helpGeneral10.1093/nar/gks109123175607PMC3531064PrimaryGenOuestInstituteProviderGenOuestsupport@genouest.orghttp://www.genouest.orgPersonPrimary contactwebPRANKMultiple sequence alignment tool.http://www.ebi.ac.uk/goldman-srv/webprank/webprankbiotools:webprank1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacGoldman ToolsEBI Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/goldman-srv/webprank/General10.1186/1471-2105-11-57921110866PMC3009689PrimaryGoldman groupPersonDeveloperAri LoytynojaPersonDeveloperNick GoldmanContributorEMBL-EBIInstituteProviderari@ebi.ac.ukPersonPrimary contactAri Loytynojaari.loytynoja@helsinki.fiPersonPrimary contactSASAnnotation of protein sequence with structural info from similar proteins in the PDB.http://www.ebi.ac.uk/thornton-srv/databases/sassasbiotools:sas1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2976Protein sequenceThe ouput is an alignment of the query sequence vs a sequence from PDB, annotated by structural datahttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/sasGeneral10.1093/protein/11.10.8559862203PrimaryRoman LaskowskiPersonDeveloperThornton GroupPersonDeveloperDuncan MilburnContributorEMBL-EBIInstituteProviderroman@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactleBIBIpqpThe BioInformatics Prokaryotes Quick Phylogeny is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence. It is also giving the useful informations if species identification is needed.https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgilebibipqpbiotools:lebibipqp6.0Web applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacFree of chargehttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0258Sequence alignment analysishttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1056Database namehttps://umr5558-bibiserv.univ-lyon1.fr/BIBIDOCNEW/index.html#lebibi-qbpp-documentationGeneral10.1186/s12859-015-0692-z26264559PMC4531848IFB ELIXIR-FRInstituteProviderJean-Pierre Flandroisjean-pierre.flandrois@univ-lyon1.frPersonPrimary contactSeaViewMultiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences.http://doua.prabi.fr/software/seaviewseaviewbiotools:seaview4Command-line toolDesktop applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0084PhylogenyLinuxWindowsMachttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0326Phylogenetic tree editinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0540Phylogenetic tree generation (from molecular sequences)http://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0872Phylogenetic treehttp://doua.prabi.fr/software/seaviewSoftware cataloguehttp://doua.prabi.fr/main/indexGeneral10.1093/molbev/msp25919854763PrimaryIFB ELIXIR-FRInstituteProviderManolo Gouymgouy@biomserv.uni-lyon1.frPersonPrimary contactrnaSeqMapA library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time.http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.htmlrnaseqmapbiotools:rnaseqmap2.32.0Command-line toolLibraryhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacRGPL-2.0BioConductorhttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://bioconductor/packages/release/bioc/src/contrib/rnaSeqMap_2.32.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/rnaSeqMap.htmlUser manual10.1186/1471-2105-12-20021612622PMC3128033PrimaryMichal Okoniewskimichal@fgcz.ethz.chPersonPrimary contactBSgenomeInfrastructure shared by all the Biostrings-based genome data packages.http://bioconductor.org/packages/release/bioc/html/BSgenome.htmlbsgenomebiotools:bsgenome1.42.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementLinuxWindowsMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1919Sequence record formathttp://bioconductor/packages/release/bioc/src/contrib/BSgenome_1.42.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/BSgenome.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherH. Pagèshpages@fredhutch.orgPersonPrimary contactUniProt AlignMultiple sequence alignment.http://www.uniprot.org/alignuniprot_alignbiotools:uniprot_align1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCC-BY-ND-3.0UniProt ToolsEBI Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://www.uniprot.org/contactHelpdeskhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.uniprot.org/help/sequence-alignmentsGeneralhttp://www.uniprot.org/help/licenseTerms of use10.1093/nar/gku98925348405PMC4384041PrimaryUniProt Consortiumhttp://www.uniprot.org/help/aboutInstituteProviderEMBL-EBIhttp://www.ebi.ac.uk/InstituteProviderhttp://www.uniprot.org/contactPersonPrimary contactXavier Watkinswatkins@ebi.ac.ukPersonPrimary contactBiostringsMemory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.http://bioconductor.org/packages/release/bioc/html/Biostrings.htmlbiostringsbiotools:biostrings2.42.1Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementLinuxWindowsMacRArtistic-2.0BioConductorFree of chargehttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_3115Microarray metadatahttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/format_1919Sequence record formathttp://bioconductor/packages/release/bioc/src/contrib/Biostrings_2.42.1.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/Biostrings.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherH. Pagèshpages@fredhutch.orgPersonPrimary contactPhymyco-DBA database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses.http://phymycodb.genouest.org/phymyco-dbbiotools:phymyco-dbDatabase portalhttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacFree of chargehttp://edamontology.org/operation_2928Alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTASequence alignmenthttp://phymycodb.genouest.org/General10.1371/journal.pone.004311723028445PMC3441585PrimaryGenOuestInstituteProviderGenOuestsupport@genouest.orgPersonPrimary contactEnsembl Genomes Fungi sequence searchSearches Ensembl Fungi sequences using Exonerate.http://fungi.ensembl.org/Multi/enasearchensembl_genomes_fungi_sequence_searchbiotools:ensembl_genomes_fungi_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://fungi.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Protists sequence searchSearches Ensembl Protists sequences using Exonerate.http://protists.ensembl.org/Multi/enasearchensembl_genomes_protists_sequence_searchbiotools:ensembl_genomes_protists_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://protists.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Metazoa sequence searchSearches Ensembl Metazoa sequences using Exonerate.http://metazoa.ensembl.org/Multi/enasearchensembl_genomes_metazoa_sequence_searchbiotools:ensembl_genomes_metazoa_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://metazoa.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl Genomes teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Plants sequence searchSearch Ensembl Plants sequences with Exonerate.http://plants.ensembl.org/Multi/enasearchensembl_genomes_plants_sequence_searchbiotools:ensembl_genomes_plants_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://plants.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl Genomes teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Bacteria sequence searchSearches Ensembl Bacteria sequences using Exonerate.http://bacteria.ensembl.org/Multi/enasearchensembl_genomes_bacteria_sequence_searchbiotools:ensembl_genomes_bacteria_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://bacteria.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl Genomes teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactClustalO WS (jabaws)JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview.http://www.compbio.dundee.ac.uk/jabawsclustalo_ws_jabawsbiotools:clustalo_ws_jabaws1Web servicehttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavaclustalJABAWShttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttps://www.biocatalogue.org/services/3687Software cataloguehttp://www.compbio.dundee.ac.uk/jabaws/man_about.htmlUser manualhttp://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/ClustalOWS.htmlAPI documentation10.1093/bioinformatics/btr30421593132PMC3129525PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://www.compbio.dundee.ac.uk/jabaws/contacts.htmlPersonPrimary contactClustal WS (jabaws)Finds the best global alignment for a set of input sequences (nucleic acid or protein).http://www.compbio.dundee.ac.uk/jabaws/clustal_ws_jabawsbiotools:clustal_ws_jabaws1Web servicehttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavaclustalJABAWShttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttps://www.biocatalogue.org/services/3760Software cataloguehttp://www.compbio.dundee.ac.uk/jabaws/man_about.htmlUser manualhttp://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/ClustalWS.htmlAPI documentation10.1093/bioinformatics/btr30421593132PMC3129525ReviewBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://www.compbio.dundee.ac.uk/jabaws/contacts.htmlPersonPrimary contactT-CoffeeA multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.http://www.tcoffee.org/Projects/tcoffee/tcoffeebiotools:tcoffee1Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacGPL-3.0T-CoffeeMatureFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttps://www.biocatalogue.org/services/3720Software cataloguehttp://www.tcoffee.org/Projects/tcoffee/#DOWNLOADDownloads pagehttp://www.tcoffee.org/Projects/tcoffee/Generalhttp://www.tcoffee.org/Projects/tcoffee/#INSTALLATIONInstallation instructionshttp://www.tcoffee.org/Projects/tcoffee/documentation/READMEGeneralT-Coffee README filehttp://www.tcoffee.org/Projects/tcoffee/#FAQFAQ10.1006/jmbi.2000.404210964570PrimaryCedric Notredamecedric.notredame@gmail.comPersonPrimary contactMuscle WS (jabaws)Multiple sequence algnment tool.http://www.compbio.dundee.ac.uk/jabawsmuscle_ws_jabawsbiotools:muscle_ws_jabaws1Web servicehttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavaMUSCLEJABAWShttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttps://www.biocatalogue.org/services/3759Software cataloguehttp://www.compbio.dundee.ac.uk/jabaws/man_about.htmlUser manualhttp://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/MuscleWS.htmlAPI documentation10.1093/bioinformatics/btr30421593132PMC3129525ReviewBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://www.compbio.dundee.ac.uk/jabaws/contacts.htmlPersonPrimary contactBWAFast, accurate, memory-efficient aligner for short and long sequencing readshttp://bio-bwa.sourceforge.netbwabiotools:bwaCommand-line toolWorkbenchhttp://edamontology.org/topic_0102MappingLinuxMacCMITBWAMaturehttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAIndex database sequences in the FASTA format. databasehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_3210Genome indexhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQAlign 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the algorithm works by seeding alignments with maximal exact matches (MEMs) and then extending seeds with the affine-gap Smith-Waterman algorithm (SW). The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picards markDuplicates does not work with split alignments. One may consider to use option -M to flag shorter split hits as secondary.http://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1332FASTA search results formathttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQFind the SA coordinates of the input reads. reference sequence query sequencehttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2044SequenceGenerate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen reference sequence query sequencehttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQGenerate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. reference sequencehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQAlign query sequences in the in.fq file reference sequencehttps://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_index.cwlTool wrapper (CWL)https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_mem.cwlTool wrapper (CWL)https://docker-ui.genouest.org/app/#/container/bioconda/bwaContainer filehttps://anaconda.org/bioconda/bwaContainer filehttp://bio-bwa.sourceforge.net/bwa.shtmlUser manual10.1093/bioinformatics/btp32419451168PMC2705234Primary10.1186/1471-2105-14-18423758764PMC3694458Benchmarking study10.1016/j.ygeno.2017.03.0012828614710.1186/1471-2164-15-26424708189PMC4051166Benchmarking study10.1093/bioinformatics/btu1462462685410.1093/bioinformatics/btp69820080505PMC2828108bwa teambio-bwa-help@sourceforge.netPersonPrimary contactHeng Lime@liheng.orghttp://www.liheng.org/http://orcid.org/0000-0003-4874-2874PersonContributorIPK BLAST ServerA homology search against the current barley sequences resources is provided. The complete sequences data set comprises the whole genome shotgun assemblies of the cultivars Morex, Barke and Bowman as well as the high and low confidence gene sets. The newest POPSEQ anchoring data is integrated. Furthermore, the barley exome capture targets are provided. Additionally, resources like bacterial artificial chromosome assemblies, BAC end sequences and full length cDNAs are included.http://webblast.ipk-gatersleben.deipk_blastbiotools:ipk_blast1Web applicationhttp://edamontology.org/topic_3053GeneticsLinuxJavadenbi-gcbnde.NBIBLASThttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_2546FASTA-likehttp://dx.doi.org/10.3835/plantgenome2015.06.0038Citation instructionshttp://webblast.ipk-gatersleben.de/barley_ibsc/docs/blast_databases.htmlGeneralhttp://webblast.ipk-gatersleben.de/ryeselect/docs/blast_databases.htmlGeneralblastuses10.3835/plantgenome2015.06.003827898761PrimaryLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenInstituteProvideripkInstituteProviderDr. Uwe Scholzscholz@ipk-gatersleben.deMaintainerDr. Uwe Scholzscholz@ipk-gatersleben.dePersonPrimary contactEnsembl Genomes Metazoa BlastSearches Ensembl Metazoa sequences using Exonerate.http://metazoa.ensembl.org/Multi/blastviewensembl_genomes_metazoa_blastbiotools:ensembl_genomes_metazoa_blast1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacBLASTEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://metazoa.ensembl.org/info/website/help/index.htmlGeneralblastuses10.1093/nar/gkv115726687719PMC4702834OtherEnsembl teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Plants BlastSearch Ensembl Plants sequences with WU-BLAST.http://plants.ensembl.org/Multi/blastviewensembl_genomes_plants_blastbiotools:ensembl_genomes_plants_blast1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacBLASTEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://plants.ensembl.org/info/website/help/index.htmlGeneralblastuses10.1093/nar/gkv115726687719PMC4702834OtherEnsembl teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactWAREasy-to-use webserver that makes it possible to simultaneously use the best methods for aligning and predicting the consensus secondary structure for a set of non-coding RNA sequences.http://genome.ku.dk/resources/war/warbiotools:war1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1961Stockholm formathttp://genome.ku.dk/resources/war/pages/about.phpGeneral10.1093/nar/gkn27518492721PMC2447782Primarybinf.ku.dkInstituteProviderStinus Lindgreenstinus@binf.ku.dkPersonPrimary contactIMGT 2Dstructure-DBIMGT/2Dstructure-DB is the IMGT® database for 2D structures (IMGT Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins and related proteins of the immune system (RPI).
Annotation is based on the IMGT-ONTOLOGY concepts.http://www.imgt.org/3Dstructure-DB/IMGT_2Dstructure-DBbiotools:IMGT_2Dstructure-DBDatabase portalhttp://edamontology.org/topic_3930Immunogeneticshttp://edamontology.org/topic_3948ImmunoinformaticsLinuxWindowsMacPerlMatureFree of charge (with restrictions)http://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_2416Protein secondary structure analysishttp://edamontology.org/data_0842Identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2858Ontology concepthttp://edamontology.org/format_2330Textual formathttp://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtmlUser manualimgtincludedIn10.1093/nar/gku105625378316PMC4383898Patrice Durouxpatrice.duroux@igh.cnrs.frPersonIMGT 3Dstructure-DBIMGT/3Dstructure-DB is the IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA).
Annotation is based on the IMGT-ONTOLOGY concepts.http://www.imgt.org/3Dstructure-DB/imgt_3dstructurebiotools:imgt_3dstructureDatabase portalhttp://edamontology.org/topic_3948Immunoinformaticshttp://edamontology.org/topic_0804Immunologyhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3930ImmunogeneticsLinuxWindowsMacPerlMatureFree of charge (with restrictions)http://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_0245Protein structural motif recognitionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0842Identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2858Ontology concepthttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_2330Textual formathttp://www.imgt.org/download/3Dstructure-DB/Downloads pagehttp://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtmlUser manualhttp://www.imgt.org/3Dstructure-DB/doc/progversion.htmlRelease notesIMGT/3Dstructure-DB and IMGT/2Dstructure-DB program versionshttp://www.imgt.org/3Dstructure-DB/doc/datarelease.htmlRelease noteshttp://www.imgt.org/3Dstructure-DB/doc/datarelease.htmlimgtincludedIn10.1093/nar/gkp94619900967PMC280894810.1093/nar/gkh04214681396PMC30877610.1101/pdb.prot56372163277410.1093/nar/gku105625378316PMC4383898Marie-Paule Lefrancmarie-paule.lefranc@igh.cnrs.frPersonPrimary contactPatrice Durouxpatrice.duroux@igh.cnrs.frSofia Kossidasofia.kossida@igh.cnrs.frIMGT Allele-AlignIMGT/Allele-Align is the IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences.http://www.imgt.org/Allele-Align/IMGT_Allele-Alignbiotools:IMGT_Allele-AlignWeb applicationhttp://edamontology.org/topic_0804Immunologyhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacPerlMatureFree of charge (with restrictions)http://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2330Textual formatimgtincludedIn150897511597200410.1093/nar/gku105625378316PMC4383898Patrice Durouxpatrice.duroux@igh.cnrs.frIMGT JunctionAnalysisIMGT/JunctionAnalysis is the IMGT® tool for the analysis of the nucleotide sequences of the V-J and V-D-J junctions of the variable domains of the immunoglobulins (IG) or antibodies and T cell receptors (TR).
Analysis is based on the IMGT-ONTOLOGY concepts.http://www.imgt.org/IMGT_jctaIMGT_JunctionAnalysisbiotools:IMGT_JunctionAnalysisWeb applicationhttp://edamontology.org/topic_3948Immunoinformaticshttp://edamontology.org/topic_3930ImmunogeneticsLinuxWindowsMacJavaMatureFree of charge (with restrictions)http://edamontology.org/operation_0448Sequence alignment analysis (conservation)http://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2200FASTA-like (text)http://www.imgt.org/IMGT_jcta/user_guideUser manualimgtincludedIn10.1093/bioinformatics/bth9451526282310.1101/pdb.prot56342163277710.1093/nar/gku105625378316PMC4383898Véronique Giudicelliveronique.giudicelli@igh.cnrs.frPersonPatrice Durouxpatrice.duroux@igh.cnrs.frPersonMarie-Paule Lefrancmarie-paule.lefranc@igh.cnrs.frPersonSofia Kossidasofia.kossida@igh.cnrs.frPersonIMGT V-QUESTIMGT/V-QUEST is the IMGT® tool for nucleotide sequence alignment and analysis of immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains, integrates IMGT/JunctionAnalysis, IMGT/Automat and IMGT/Collier-de-Perles.
Analysis is based on the IMGT-ONTOLOGY concepts.http://www.imgt.org/IMGT_vquestimgt_v-questbiotools:imgt_v-questWeb applicationhttp://edamontology.org/topic_3948Immunoinformaticshttp://edamontology.org/topic_3930Immunogeneticshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168SequencingLinuxWindowsMacJavaMatureFree of charge (with restrictions)http://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0258Sequence alignment analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_0448Sequence alignment analysis (conservation)http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://www.imgt.org/IMGT_vquest/user_guideUser manualhttp://www.imgt.org/IMGT_vquest/program_versionsRelease notesIMGT/V-QUEST program versionshttp://www.imgt.org/IMGT_vquest/data_releasesRelease notesIMGT/V-QUEST reference directory releasesimgtincludedIn10.1093/nar/gkn31618503082PMC244774610.1093/nar/gkh41215215425PMC44155010.1101/pdb.prot56332163277810.1093/nar/gku105625378316PMC4383898Marie-Paule LefrancMarie-Paule.Lefranc@igh.cnrs.frPersonPrimary contactVéronique Giudicelliveronique.giudicelli@igh.cnrs.frPersonPatrice Durouxpatrice.duroux@igh.cnrs.frPersonSofia Kossidasofia.kossida@igh.cnrs.frPersonClustal 1.8 (Clustal W, Clustal X)Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV).http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/clustalwbiotools:clustalw1.8 - 1.83Command-line toolDesktop applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacclustalLegacyhttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/Downloads pageArchived old versions.1.8 - 1.83clustal2hasNewVersion10.1093/nar/22.22.46737984417PMC308517Primaryhistorical CLUSTAL WHistorical publication on CLUSTAL W. Open access to PDF only.10.1093/nar/25.24.48769396791PMC147148Primaryhistorical CLUSTAL XHistorical publication on CLUSTAL X. Open access.10.1093/nar/gkg50012824352PMC168907Primary1.83Short overview article, with some new features of Clustal, Clustal X, and other associated software nad services. Open access.10.1093/bioinformatics/8.2.1891591615Otherhistorical CLUSTALHistorical publication on CLUSTAL. Closed access.10.1016/0378-1119(88)90330-7Otherhistorical CLUSTALHistorical publication on CLUSTAL. Closed access.Clustal helpdeskclustalw@ucd.ieDivisionPrimary contactsetuppromoterBuilds a fasta file of sequences from a reference genome using promoter region coordinates.https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/setuppromoter/1.0setuppromoterbiotools:setuppromoter1.0Web applicationhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacPerlgalaxyPasteurInstitut PasteurMatureOpen accesshttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/setuppromoter/1.0Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Fpromoteur_tools%2Fsetuppromoter%2F1.0General10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactchangenameChange the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files.https://urgi.versailles.inra.fr/Tools/REPETchangenamebiotools:changename1.0.0Web applicationhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacgalaxyPasteurREPETMatureOpen accesshttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2305GFFhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_2573SAMhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/changeName/1.0.0Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Furgi_tools%2FchangeName%2F1.0.0General10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactrestrictsequencelistKeep the elements of a list of sequences whose name is mentionned in a given file.https://urgi.versailles.inra.fr/Tools/REPETrestrictsequencelistbiotools:restrictsequencelist1.0.0Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacgalaxyPasteurREPETMatureOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2330Textual formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/restrictSequenceList/1.0.0Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Furgi_tools%2FrestrictSequenceList%2F1.0.0General10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactmodifysequencelistExtend or shring a list of sequences.https://urgi.versailles.inra.fr/Tools/REPETmodifysequencelistbiotools:modifysequencelist1.0.0Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacgalaxyPasteurMatureOpen accesshttp://edamontology.org/operation_0369Sequence cuttinghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/modifySequenceList/1.0.0Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Furgi_tools%2FmodifySequenceList%2F1.0.0General10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactfrogs_clusteringThis tool uses an iterative growth process and the use of sequence abundance values to delineate OTUs.http://frogs.toulouse.inra.fr/frogs_clusteringbiotools:frogs_clustering2.3.0Web applicationhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3174MetagenomicsLinuxWindowsMacgalaxyPasteurFROGSMatureOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/mvalade/frogs/FROGS_clustering/2.3.0Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fmvalade%2Ffrogs%2FFROGS_clustering%2F2.3.0General10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactfrogs_normalisationKeeps in each sample the same number of element by random sampling.http://frogs.toulouse.inra.fr/frogs_normalisationbiotools:frogs_normalisation1.1.0Web applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3301MicrobiologyLinuxWindowsMacgalaxyPasteurFROGSMatureOpen accesshttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3464JSONhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/mvalade/frogs/FROGS_normalisation/1.1.0Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fmvalade%2Ffrogs%2FFROGS_normalisation%2F1.1.0General10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactclc_unmapped_readsOutput the unmapped reads.https://bio.tools/clcbio_genomics_workbenchclc_unmapped_readsbiotools:clc_unmapped_reads4.010.83648Web applicationhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacgalaxyPasteurCLC Main WorkbenchMatureOpen accesshttp://edamontology.org/operation_2520DNA mappinghttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2333Binary formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/clc_assembly_4/clc_unmapped_reads/4.010.83648Galaxy service10.1186/1471-2164-11-57120950480PMC3091720Review10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactclc_find_variationsFind positions where the reads indicate a consistent difference from the reference sequences. Optionally, consensus sequences can be written to a fasta file.https://bio.tools/clcbio_genomics_workbenchclc_find_variationsbiotools:clc_find_variations4.4.2Web applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0199Genetic variationLinuxWindowsMacgalaxyPasteurCLC Main WorkbenchMatureOpen accesshttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2333Binary formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/clc_assembly_4/clc_find_variations/4.4.2Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Fclc_assembly_4%2Fclc_find_variations%2F4.4.2User manual10.1186/1471-2164-11-57120950480PMC3091720Review10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactclc_assemblerDe novo assembly algorithm of CLC Assembly Cell for both short and long reads.https://bio.tools/clcbio_genomics_workbenchclc_assemblerbiotools:clc_assembler4.4.2Web applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0196Sequence assemblyLinuxWindowsMacgalaxyPasteurCLC Main WorkbenchMatureOpen accesshttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3284SFFhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/clc_assembly_4/clc_assembler/4.4.2Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Fclc_assembly_4%2Fclc_assembler%2F4.4.2General10.1002/ange.201507047Other10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactcropA clustering tool which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU).https://code.google.com/archive/p/crop-tingchenlab/cropbiotools:crop1.33Web applicationhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3174MetagenomicsLinuxWindowsMacgalaxyPasteurMatureOpen accesshttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/CROP/1.33Galaxy service10.1093/bioinformatics/btq72521233169PMC3042185Primary10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contact