QUASTQUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.http://quast.sourceforge.net/quastquastbiotools:quastv.5.3.0Workflowhttp://edamontology.org/topic_0196Sequence assemblyLinuxMacPerlPythonCGPL-2.0ONTeaterMatureFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3180Sequence assembly validationhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTA# Running quast on a eukaryotic genomequast -ek assembly.fa --out output_prefixhttps://github.com/ablab/quastRepositoryhttps://github.com/ablab/quast/issuesIssue trackerhttp://quast.bioinf.spbau.ru/General10.1093/bioinformatics/btt08623422339PMC3624806QUAST Supportquast.support@cab.spbu.ruPersonPrimary contactblast2galaxyblast2galaxy is a Python package providing a CLI and API for performing BLAST+ and DIAMOND searches on Galaxy servers. It allows users to leverage the Galaxy API for sequence alignments and is available through package managers like Bioconda and Docker.https://blast2galaxy.readthedocs.ioblast2galaxybiotools:blast2galaxyhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0154Small moleculesPythonCMIThttp://edamontology.org/operation_2421Database search10.1093/BIOADV/VBAE18539659591PMC11629687Patrick Königkoenig@ipk-gatersleben.dehttps://orcid.org/0000-0002-8948-6793PersonPlastParallel 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_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2330Textual format

Sequence alignmenthttps://plast.inria.fr/General10.1186/1471-2105-10-32919821978PMC2770072PrimaryGenOuestInstituteProviderDominique Lavenierlavenier@irisa.frPersonPrimary contactBESSTThis tool is a scaffolder. The input is a contig file and a set of BAM files from mapping paired-ends and/or mate-pair reads to the contigs, and the output are scaffolds, i.e., the contigs linked and oriented. It is both fast and accurate. Careful estimation of the gaps between contigs, many other scaffolders have seriously biased estimation. Novel treatment of paired-end contamination in mate-pair libraries, which identifies that some links in the MP data are better treated as PE.https://github.com/ksahlin/BESSTbesstbiotools:besst1Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyLinuxMacPythonGPL-3.0MatureFree of chargehttp://edamontology.org/operation_3216Scaffoldinghttps://github.com/ksahlin/BESSTRepositoryhttps://github.com/ksahlin/BESSTGeneral10.1186/1471-2105-15-28125128196PMC4262078Primary10.1101/025650Other10.1093/bioinformatics/bts44122923455Othernada.su.seInstituteProviderKristoffer Sahlinhttps://github.com/ksahlin/BESST/issuesPersonPrimary contactBASEA comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis.http://base.thep.lu.sebasebiotools:base1Web applicationhttp://edamontology.org/topic_3071Data managementLinuxWindowsMachttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2603Gene expression data

http://edamontology.org/data_2603Gene expression data

http://base.thep.lu.se/#DocumentationGeneral10.1186/1471-2105-10-33019822003PMC2768720Primarybils.seInstituteProviderhttp://base.thep.lu.se/wiki/MailingListsPersonPrimary contactBFASTBlat-like Fast Accurate Search Tool.https://sourceforge.net/projects/bfastbfastbiotools:bfastCommand-line toolhttp://edamontology.org/topic_3673Whole genome sequencingLinuxMacCGPL-3.0Maturehttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttps://sourceforge.net/p/bfast/wiki/Home/General10.1186/1471-2105-10-17519508732PMC2709925Nils Homerhttps://sourceforge.net/u/nilshomer/profile/PersonPrimary contactBLESSBLoom-filter-based Error correction Solution for high-throughput Sequencing reads is a novel algorithm that produces accurate correction results with much less memory compared with previous solutions.https://sourceforge.net/p/bless-ec/wiki/Home/blessbiotools:blessCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0654DNALinuxC++http://edamontology.org/operation_3195Sequencing error detectionhttp://www.mybiosoftware.com/bless-v0p17-bloom-filter-based-error-correction-tool-for-ngs-reads.htmlSoftware cataloguehttps://sourceforge.net/p/bless-ec/wiki/Home/General10.1093/bioinformatics/btu03024451628PMC6365934Anand Ramachandranaramach4@illinois.eduhttp://compbio.bioen.illinois.edu/index.htmlPersonPrimary contactBlasrSoftware for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.https://github.com/PacificBiosciences/blasrblasrbiotools:blasrCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622GenomicsLinuxShellC++PerlPythonhttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/operation_2429Mappinghttp://www.mybiosoftware.com/blasr-basic-local-alignment-successive-refinement.htmlSoftware cataloguehttps://github.com/PacificBiosciences/blasrGeneral10.1186/1471-2105-13-23822988817PMC3572422support@pacb.comhttp://www.smrtcommunity.com/PersonPrimary contactclaspA fast and flexible fragment chainer that supports linear and sum-of-pair gap costs and uses highly time-efficient index structure, i.e., Johnson priority queues and range trees padded with Johnson priority queues. Chaining of short match fragments helps to quickly and accurately identify region of synteny that may not be found using common local alignment heuristics alone.http://www.bioinf.uni-leipzig.de/Software/clasp/claspbiotools:clasp1.1Command-line toolhttp://edamontology.org/topic_0102Syntenyhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0196Sequence assemblyLinuxhttp://edamontology.org/operation_0495Local alignmenthttp://www.mybiosoftware.com/clasp-1-1-local-fragment-chainer-sum-of-pair-gap-costs.htmlSoftware cataloguehttp://www.bioinf.uni-leipzig.de/Software/clasp/clasp.htmlGeneral10.1186/1748-7188-6-421418573PMC3072320Primarychristian@bioinf.uni-leipzig.dehttp://hoffmann.bioinf.uni-leipzig.de/LIFE/Christian.htmlPersonPrimary contactDFASTFlexible prokaryotic genome annotation pipeline for faster genome publication.https://dfast.nig.ac.jp/dfastbiotools:dfastCommand-line toolWeb applicationhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacPythonGPL-3.0http://edamontology.org/operation_0362Genome annotationhttps://dfast.nig.ac.jp/faqGeneral10.1093/bioinformatics/btx71329106469PMC5860143Yasukazu Nakamurayn@nig.ac.jpPersonPrimary contactRIblastAn ultrafast RNA–RNA interaction prediction system based on a seed-and-extension approach.https://funpopgen.github.io/veqtl-mapper/riblastbiotools:riblastCommand-line toolhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0099RNALinuxMacC++MIThttp://edamontology.org/operation_0272Residue interaction predictionhttps://github.com/fukunagatsu/RIblastGeneral10.1093/bioinformatics/btx28728459942PMC5860064Tsukasa Fukunagt.fukunaga@kurenai.waseda.jpPersonPrimary contactMichiaki Hamadamhamada@waseda.jpPersonPrimary contactBARTTranscription factor prediction tool with query gene sets or epigenomic profiles.http://faculty.virginia.edu/zanglab/bart/bartbiotools:bartCommand-line toolhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3173EpigenomicsLinuxMacPythonhttp://edamontology.org/operation_0438Transcriptional regulatory element predictionhttp://faculty.virginia.edu/zanglab/bart/#tutorialGeneral10.1093/bioinformatics/bty19429608647PMC6084568Chongzhi Zangzang@virginia.eduPersonPrimary contactFLASHIdentifies paired-end reads which overlap in the middle, converting them to single long readshttp://ccb.jhu.edu/software/FLASH/flashbiotools:flashCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0196Sequence assemblyLinuxChttp://edamontology.org/operation_3219Read pre-processinghttp://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/operation_0310Sequence assembly10.1093/bioinformatics/btr50721903629PMC3198573FLASh teamflash.comment@gmail.comPersonPrimary contactblastprodomRecursive psi-blast against the ProDom database.http://prodom.prabi.fr/prodom/current/documentation/blastProDom.htmlblastprodombiotools:blastprodom1Web servicehttp://edamontology.org/topic_0080Sequence analysisBLASThttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_0857Sequence search results

https://www.biocatalogue.org/services/414Software cataloguehttp://prodom.prabi.fr/prodom/current/documentation/blastProDom.htmlGeneral10.1093/bioinformatics/btg11112724303OtherBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://prodom.prabi.fr/prodom/current/html/home.phpPersonPrimary contactBlastRA new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. We have shown that this approach has better sensitivity and specifity than other softwares with comparable computational cost.http://www.tcoffee.org/Projects/blastr/blastrbiotools:blastr2.2Command-line toolhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_3345Data identity and mappinghttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNALinuxPerlBLASThttp://edamontology.org/operation_0338Sequence database searchhttp://www.mybiosoftware.com/blastr-2-1-searching-clustering-rna.htmlSoftware cataloguehttp://www.tcoffee.org/Projects/blastr/#COMMANDSGeneral10.1093/nar/gkr33521624887PMC3167602Primaryhttp://www.tcoffee.org/Projects/blastr/#CONTACTPersonPrimary contactBLAST2SRSTool to retrieve protein sequences using similarity (BLAST) and keyword searches.http://blast2srs.embl.de/blast2srsbiotools:blast2srsWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3168SequencingBLASThttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0968Keyword

http://edamontology.org/data_0857Sequence search results

blastuses10.1093/nar/gkg53512824420PMC168942BLASTOModified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.http://oxytricha.princeton.edu/BlastO/index.htmlblastobiotools:blastoWeb applicationhttp://edamontology.org/topic_0080Sequence analysisBLASThttp://edamontology.org/operation_0346Sequence similarity searchblastuses10.1093/nar/gkm27817483516PMC1933156Laura F. Landweberlfl@princeton.eduPersonPrimary contactH-BLASTFast protein sequence alignment toolkit on heterogeneous computers with GPUs .https://github.com/Yeyke/H-BLASTh-blastbiotools:h-blastCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacBLASThttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_0857Sequence search results

https://github.com/Yeyke/H-BLASTGeneralblastuses10.1093/bioinformatics/btw76928087515Yuesheng Xuyux06@syr.eduPersonPrimary contactblast_best_scoreReturns the list best hits from a list of BLAST results.https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/pgp_tools/blast_best_score/0.0.1blast_best_scorebiotools:blast_best_score0.0.1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacBLAST utilityInstitut PasteurgalaxyPasteurMatureOpen accesshttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_3475TSV

http://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSV

https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/pgp_tools/blast_best_score/0.0.1Galaxy servicehttps://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fodoppelt%2Fpgp_tools%2Fblast_best_score%2F0.0.1General10.1016/S0022-2836(05)80360-2Other10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactBLANTBasic Local Alignment for Networks Tool.https://github.com/waynebhayes/BLANTBLANTbiotools:BLANTCommand-line toolhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0084PhylogenyLinuxMacCUnlicenseMatureFree of chargeOpen accesshttps://github.com/waynebhayes/BLANT/issuesIssue trackerhttps://github.com/waynebhayes/BLANT/releasesSource codehttps://github.com/waynebhayes/BLANT/blob/master/README.mdGeneral10.1093/bioinformatics/btz60331373347PrimaryWayne B. Hayeswhayes@uci.eduPersonPrimary contactOMBlastAlignment tool for optical mapping using a seed-and-extend approach.https://github.com/TF-Chan-Lab/OMBlastOMBlastbiotools:OMBlastCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_2885DNA polymorphismLinuxWindowsJavaGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/operation_3798Read binninghttp://edamontology.org/operation_3216Scaffoldinghttps://github.com/TF-Chan-Lab/OMBlast/issuesRepositoryhttps://github.com/TF-Chan-Lab/OMBlast/blob/master/OMBlastManual.pdfUser manualhttps://github.com/TF-Chan-Lab/OMBlast/blob/master/README.mdGeneral10.1093/bioinformatics/btw62028172448PMC5409310PrimaryKevin Y. Yipkevinyip@cse.cuhk.edu.hkPersonPrimary contactTing-Fung Chantf.chan@cuhk.edu.hkPersonPrimary contactPlassProtein-Level ASSembler (PLASS): sensitive and precise protein assemblerhttps://plass.mmseqs.comPlassbiotools:Plass4-687d73-764a32-c7e351-2e0efCommand-line toolhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3308TranscriptomicsLinuxMacC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

Assemble proteins from paired-end readsplass assemble reads_1.fastq.gz reads_2.fastq.gz assembly.fas tmphttps://github.com/soedinglab/plass/issuesIssue trackerhttps://github.com/soedinglab/plassRepositoryhttps://mmseqs.com/plass/plass-static_sse41.tar.gzBinariesLatest git static build for linuxhttps://mmseqs.com/plass/plass-osx-sse41.tar.gzBinariesLatest git static build for macOShttps://hub.docker.com/r/soedinglab/plassContainer filemmseqs2uses10.1038/s41592-019-0437-431235882Other10.1101/386110OtherMartin Steineggerhttp://orcid.org/0000-0001-8781-9753PersonPrimary contactDeveloperMaintainerMilot Mirditahttp://orcid.org/0000-0001-8637-6719PersonDeveloperMaintainerJohannes Södinghttp://orcid.org/0000-0001-9642-8244PersonPrimary contactBJASSA new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates | Liu, Y., Chen, X., & Li, G. (2019). A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates. Statistical methods in medical research, 0962280219864710 | This program implements the BJASS joint screening method for DLBCL data (stored in matlab.mat) described in Section 4 of the paperhttps://github.com/yiucla/BJASSBJASSbiotools:BJASSMATLABhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_3557Imputationhttp://edamontology.org/operation_3659Regression analysis10.1177/096228021986471031359834PMC8285086BlastFrostBlastFrost is a highly efficient method for querying 100,000s of genome assemblies. BlastFrost builds on the recently developed Bifrost, which generates a dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants.https://github.com/nluhmann/BlastFrostblastfrostbiotools:blastfrostCommand-line toolhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0622GenomicsC++PythonGPL-3.0http://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotyping10.1101/2020.01.21.914168Primary10.1186/s13059-020-02237-333430919PMC7798312PrimaryNina LuhmannN.Luhmann@warwick.ac.ukPersonBLATFast, accurate spliced alignment of DNA sequences.http://genome.ucsc.edu/cgi-bin/hgBlat?command=startblatbiotools:blatRRID:SCR_011919rridWeb applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacChttp://edamontology.org/operation_0292Sequence alignmenthttp://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlignGeneral10.1101/gr.22920211932250PMC187518Website and data questionsgenome@soe.ucsc.eduPersonPrimary contactMirror and source code questionsgenome-mirror@soe.ucsc.eduPersonPrimary contactServer and website access problemsgenome-www@soe.ucsc.eduPersonPrimary contactLASTShort read alignment program incorporating quality scoreshttp://last.cbrc.jp/lastbiotools:lastRRID:SCR_006119rridWeb servicehttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0797Comparative genomicsLinuxWindowsMacC++GPL-3.0Maturehttp://edamontology.org/operation_0292Sequence alignmenthttp://last.cbrc.jp/doc/General10.1093/nar/gkq01020110255PMC2853142LAST Supportlast-align@googlegroups.comPersonPrimary contactVAASTVariant Annotation, Analysis and Search Toolhttp://www.yandell-lab.org/software/vaast.htmlvaastbiotools:vaastRRID:SCR_002179rridSuitehttp://edamontology.org/topic_3175DNA structural variationMaturehttp://edamontology.org/operation_3226Variant prioritisationhttp://www.yandell-lab.org/software/VAAST/VAAST_Users_Guide.pdfUser manual10.1016/j.ajhg.2011.05.01721700266PMC3135802Mark Yandellmyandell@genetics.utah.eduPersonPrimary contactPZLASTAn ultra-fast amino acid sequence similarity search server against public metagenomes.https://pzlast.riken.jp/metapzlastbiotools:pzlastWeb applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3837Metagenomic sequencinghttp://edamontology.org/topic_0154Small moleculesMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_2495Expression analysishttps://pzlast.riken.jp/meta/apiAPI documentation10.1093/bioinformatics/btab49234240105PMC8570820Hiroshi Morihmori@nig.ac.jphttps://orcid.org/0000-0003-0806-7704PersonKen Kurokawahttps://orcid.org/0000-0001-8662-9958Toshikazu Ebisuzakihttps://orcid.org/0000-0002-3918-1166Ken Kurokawahttps://orcid.org/0000-0001-8662-9958Hitoshi IshikawaBEASTThe Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov chain Monte Carlo). It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.http://beast.bio.ed.ac.uk/beastbiotools:beastCommand-line toolhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavaEBI Training Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0540Phylogenetic tree generation (from molecular sequences)http://edamontology.org/operation_0547Phylogenetic tree generation (maximum likelihood and Bayesian methods)http://beast.community/first_tutorialGeneral10.1093/molbev/mss07522367748PMC340807010.1093/ve/vey01629942656PMC600767410.1186/1471-2148-7-21417996036PMC2247476http://groups.google.com/group/beast-usersPersonPrimary contactBlast2GOBioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation.https://www.blast2go.com/blast2gobiotools:blast2goCommand-line toolDesktop applicationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsLinuxWindowsMacBLASThttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/data_1383Sequence alignment (nucleic acid)

http://edamontology.org/data_3753Over-representation data

https://www.blast2go.com/blast2go-proGeneral10.1093/bioinformatics/bti61016081474Primary10.1093/nar/gkn17618445632PMC2425479contact@biobam.comhttps://www.biobam.com/biobam-contact/PersonPrimary contactBLASTA tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.https://blast.ncbi.nlm.nih.gov/Blast.cgiblastbiotools:blastCommand-line toolWeb applicationWeb APIhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0091BioinformaticsLinuxWindowsMacBLASTMatureFree of chargeOpen accesshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_3331BLAST XML results formathttp://edamontology.org/format_3836BLAST XML v2 results formathttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_1966ASN.1 sequence formathttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_2333Binary formathttp://edamontology.org/format_2330Textual format

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocsGeneralhttps://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ReferencesCitation instructions10.1016/S0022-2836(05)80360-22231712Primary10.1093/bioinformatics/btw30527256311PMC5013910Benchmarking study10.1093/nar/gkn20118440982PMC2447716Primary10.1093/nar/gkt28223609542PMC3692093PrimaryBLAST Supportblast-help@ncbi.nlm.nih.govPersonPrimary contactBLAZEIdentification of cell barcodes from long-read single-cell RNA-seq with BLAZE.https://github.com/shimlab/BLAZEblazebiotools:blazeScripthttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0203Gene expressionMacLinuxWindowsPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3933Demultiplexinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3185Base-callinghttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3752CSV

10.1186/s13059-023-02907-y37024980PMC10077662PrimaryHeejung Shimhee.shim@unimelb.edu.auPersonMichael B. Clarkmichael.clark@unimelb.edu.auhttps://orcid.org/0000-0002-2903-9537PersonFLUSTA fast, open source framework for ultrasound blood flow simulations.http://www.ustb.no/flustflustbiotools:flustSuitehttp://edamontology.org/topic_3954Echographyhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3384Medical imagingMacLinuxWindowsMATLABFree of chargeOpen accesshttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttps://bitbucket.org/ustb/ustb/src/master/Repository10.1016/j.cmpb.2023.10760437220679PrimaryIngvild Kinn Ekrollingvild.k.ekroll@ntnu.nohttps://orcid.org/0000-0002-0540-0201MaastGenotyping thousands of microbial strains. Type SNPs from a set of whole genome assemblies and sequencing reads from beginning to end in one single command line.https://github.com/zjshi/Maastmaastbiotools:maastCommand-line toolWorkflowhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0196Sequence assemblyMacLinuxWindowsPythonC++MITFree of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_0525Genome assembly10.1186/s13059-023-03030-837563669PMC10416524Katherine S. Pollardkpollard@gladstone.ucsf.eduhttps://orcid.org/0000-0002-9870-6196PersonZhou Jason ShiPersonStephen NayfachPersonBLAST (EBI)Find regions of sequence similarity and alignments between a query sequence and database sequences.https://www.ebi.ac.uk/jdispatcher/sss/ncbiblastblast_ebibiotools:blast_ebi1Web APIWeb applicationWeb servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacBLASTEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_0857Sequence search results

https://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttps://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DownloadDownloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttps://blast.ncbi.nlm.nih.gov/Blast.cgiGeneralblastuses10.1186/1471-2105-10-42120003500PMC2803857Primary10.1093/nar/gkae24138597606PMC11223882Other10.1093/nar/gkac24035412617PMC9252731OtherEMBL-EBIInstituteProviderNCBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contacteTBLASTTextual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.http://etest.vbi.vt.edu/etblast3/etblastbiotools:etblastWeb applicationhttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_3068Literature and languagehttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0224Query and retrieval10.1093/bioinformatics/btl3881692621910.1093/nar/gkm22117452348PMC1933238blastxml_to_top_descrThis tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers.https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descrblastxml_to_top_descrbiotools:blastxml_to_top_descrWeb applicationhttp://edamontology.org/topic_0080Sequence analysisMITBLASTMatureFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_0361Sequence annotationhttps://github.com/peterjc/galaxy_blastRepositoryhttps://github.com/peterjc/galaxy_blast/issuesIssue trackerblast_rbhThis tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits.https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbhblast_rbhbiotools:blast_rbhWeb applicationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsMITBLASTMatureFree of chargeOpen accesshttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_2478Nucleic acid sequence analysis10.1186/s13742-015-0080-710.1186/1471-2105-10-421BoostBoost is a set of libraries for the C++ programming language that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.https://www.boost.org/boostbiotools:boostLibraryhttp://edamontology.org/topic_3570Pure mathematicshttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3372Software engineeringC++Otherhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_1352Regular expressionhttp://edamontology.org/format_2032Workflow formathttp://edamontology.org/data_2968Imagehttps://www.boost.org/community/groups.htmlMailing listhttps://www.boost.org/users/download/Downloads pagehttps://www.boost.org/doc/Generalhttps://www.boost.org/doc/libs/1_76_0/more/getting_started/windows.htmlInstallation instructionsGuide for Windowshttps://www.boost.org/doc/libs/1_76_0/more/getting_started/unix-variants.htmlInstallation instructionsGuide for Unix variants (MacOS, Linux)https://github.com/boostorg/wiki/wikiGeneralBLAST ViewerTool that aims at displaying in a graphical way results from the NCBI BLAST software.https://github.com/pgdurand/BlastViewerblast_viewerbiotools:blast_viewer5.5.2Desktop applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacJavaAGPL-3.0BLAST utilityMatureFree of chargeOpen accesshttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_2422Data retrievalhttps://github.com/pgdurand/BlastViewerRepositoryhttps://github.com/pgdurand/BlastViewer/releasesSoftware packagehttps://github.com/pgdurand/BlastViewer/wikiUser manualPatrick Durandhttps://github.com/pgdurand/BlastViewer/issuesPersonDeveloperPlealoghttp://www.plealog.comPersonProviderhttps://github.com/pgdurand/BlastViewer/issuesPersonPrimary contactblastxml to gapped gff3Convert BlastXML results into GFF3 format.https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/blastxml_to_gapped_gff3/blastxml_to_gapped_gff3/1.1blastxml_to_gapped_gff3biotools:blastxml_to_gapped_gff3Web applicationhttp://edamontology.org/topic_3068Literature and languageLinuxMacWindowsNot licensedFree of chargeOpen accesshttp://edamontology.org/operation_3434ConversionRMBlastRMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.http://www.repeatmasker.org/RMBlast.htmlrmblastbiotools:rmblast2.11.0Command-line toolDesktop applicationhttp://edamontology.org/topic_0622GenomicsMacLinuxC++OSL-2.1Free of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2044SequencerepeatmaskerusesArian SmitRobert HubleyJeb RosenBWASPTools and applications for integrative analysis of DNA methylation in social insects.https://BrendelGroup.org/SingularityHub/bwasp.sifbwaspbiotools:bwaspWorkflowhttp://edamontology.org/topic_3674Methylated DNA immunoprecipitationhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3518Microarray experimentShellPerlPythonGPL-2.0Free of chargeOpen accesshttp://edamontology.org/operation_3204Methylation analysishttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3192Sequence trimminghttps://github.com/BrendelGroup/BWASPRepository10.1101/2021.08.19.457008Volker P. Brendelvbrendel@indiana.eduhttps://orcid.org/0000-0002-8055-7508PersonClaire Morandinhttps://orcid.org/0000-0002-0811-901XiBLASTiBLAST is tool which performs incremental BLAST of new sequences via automated e-value correction.https://github.com/vtsynergy/iBLASTiblastbiotools:iblastCommand-line toolhttp://edamontology.org/topic_3071Biological databaseshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121ProteomicsPythonCC0-1.0http://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0292Sequence alignmenthttps://github.com/vtsynergy/iBLAST/issuesIssue tracker10.1371/JOURNAL.PONE.024941033886589PMC8062096Sajal Dashdashs@ornl.govhttps://orcid.org/0000-0001-5308-914XPersonWu-chun Fengfeng@cs.vt.eduPersonBLAST-QCBLAST-QC is a tool for automated analysis of BLAST results. It is a quality control filter and parser for NCBI BLAST XML results.https://github.com/torkian/blast-QCblast-qcbiotools:blast-qcCommand-line toolhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3372Software engineeringCJavaPythonMIThttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_1812Parsinghttp://edamontology.org/operation_0495Local alignmenthttps://github.com/torkian/blast-QC/issuesIssue tracker10.1186/S40793-020-00361-Y33902722PMC8066848PrimaryR. Sean Normanrsnorman@mailbox.sc.eduhttps://orcid.org/0000-0003-4766-4376PersonBlastKOALABlastKOALA (KEGG Orthology And Links Annotation) is a KEGG Web service for annotating genomes and understanding organisms.https://www.kegg.jp/blastkoala/blastkoalabiotools:blastkoalaWeb applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0533Expression profile pathway mappinghttps://www.kegg.jp/blastkoala/help_blastkoala.htmlQuick start guide10.1016/j.jmb.2015.11.00626585406PrimaryMinoru Kanehisakanehisa@kuicr.kyoto-u.ac.jpPersonPrimary contactBAITBAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.http://sourceforge.net/projects/bait/baitbiotools:bait1.4RRID:SCR_000511rridCommand-line toolhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3168SequencingLinuxRhttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/operation_2945Analysishttp://www.mybiosoftware.com/bait-1-0-organizing-genomes-and-mapping-rearrangements-in-single-cells.htmlSoftware cataloguehttps://sourceforge.net/p/bait/wiki/Home/General10.1038/nmeth.220623042453PMC3580294Primaryhttp://www.terryfoxlab.ca/PersonPrimary contactBAlaSBAlaS is an interactive web application for performing CASM via BudeAlaScan and visualizing its results. BAlaS is interactive and intuitive to use. Results are displayed directly in the browser for the structure being interrogated enabling their rapid inspection. BAlaS has broad applications in areas, such as drug discovery and protein-interface design.https://balas.appbalasbiotools:balasWeb applicationhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3957Protein interaction experimenthttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_3336Drug discoveryElmPythonC++MIThttp://edamontology.org/operation_3907Information extractionhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_0248Residue interaction calculationhttps://github.com/wells-wood-research/balasRepository10.1093/BIOINFORMATICS/BTAA02631930404Christopher W Woodchris.wood@ed.ac.ukPersonRichard B Sessionsr.sessions@bristol.ac.ukPersonBYASEBYASE is a Python package that uses Bayesian inference to identify gene-level and isoform-level ASE (Allele-specific expression) in polyploid (diploid or higher) organisms from single-end or paired-end RNA-seq data.https://github.com/ncjllld/byasebyasebiotools:byaseDesktop applicationLibraryhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_3512Gene transcriptsPythonGPL-3.0http://edamontology.org/operation_3454Phasinghttp://edamontology.org/operation_3223Differential gene expression analysishttp://edamontology.org/operation_3661SNP annotationhttps://github.com/ncjllld/byase_guiRepository10.1093/BIOINFORMATICS/BTAA63632678892Guohua Wangghwang@hit.edu.cnPersonBlast2FishBlast2Fish is a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. It is a novel approach for performing functional enrichment analysis on non-model teleost fish transcriptome data.http://blast2fish.ntou.edu.twblast2fishbiotools:blast2fishWeb applicationhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3644de Novo sequencinghttp://edamontology.org/operation_0524De-novo assembly10.1186/S12859-020-3507-932366294PMC7199347Ming-Wei Lumingwei@ntou.edu.twhttps://orcid.org/0000-0003-3249-5311Person