Phylo-MoviesPhylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.https://enesberksakalli.github.io/phylo-movies/phylo-moviesbiotools:phylo-movies0.98.1Desktop applicationWeb applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0092Data visualisationWindowsMacLinuxPythonJavaScriptTypeScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAVisualizes ordered phylogenetic tree series as animated transition movies with comparison, MSA context, movement analytics, image export, and recording support.https://github.com/enesBerkSakalli/phylo-moviesRepositorySource code repository.https://enesberksakalli.github.io/phylo-movies/demo/ServiceStatic browser demo with precomputed example movies.https://github.com/enesBerkSakalli/phylo-movies/issuesIssue trackerhttps://github.com/enesBerkSakalli/phylo-moviesSource codeSource checkout for full web application and backend workflows.0.98.1https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1BinariesDesktop convenience builds for macOS, Windows, and Linux.0.98.1https://enesberksakalli.github.io/phylo-movies/manual/User manualResearcher-facing manual.https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.mdGeneralProject overview, installation, usage, citation, and links.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.mdInstallation instructionsLocal source-checkout setup instructions.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.mdAPI documentationBackend API documentation.10.64898/2026.04.01.715821PrimarybioRxiv preprint describing the Phylo-Movies method and examples.10.5281/zenodo.20488923Primary0.98.1Archived software release on Zenodo.Enes Berk Sakallienes@lbi-netmed.athttps://github.com/enesBerkSakalliPersonDeveloperPrimary contactCorresponding software contact.Simon E. HaendelerPersonDeveloperArndt von HaeselerPersonDeveloperHeiko A. SchmidtPersonDeveloperSigmaCVAuto-generates clean, customizable academic CVs from open research data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations render through CSL; and the account holder is matched by persistent identifier (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source, and FAIR by design.https://sigmacv.orgsigmacvbiotools:sigmacv0.1.0Web applicationMacWindowsLinuxJavaScriptTypeScriptApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_0226Annotationhttps://github.com/BasileChretien/sigmacvRepositoryhttps://github.com/BasileChretien/sigmacv/issuesIssue trackerhttps://github.com/BasileChretien/sigmacvSource codehttps://github.com/BasileChretien/sigmacv#readmeGeneral10.5281/zenodo.20594123Other0.1.0Basile Chrétienchretien.basile.jean.bernard.u4@s.mail.nagoya-u.ac.jphttps://orcid.org/0000-0002-7483-2489DeveloperMaintainerPrimary contactNOVOPlastyNOVOPlasty - The organelle assembler and heteroplasmy caller.
NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes..https://github.com/ndierckx/NOVOPlastyNOVOPlastybiotools:NOVOPlastyNOVOPlasty4.3.5Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyPerlOtherMaturehttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3227Variant callinghttps://github.com/ndierckx/NOVOPlastyRepositoryhttps://github.com/ndierckx/NOVOPlasty/issuesIssue trackerhttps://github.com/ndierckx/NOVOPlasty/wikiGeneral10.1093/nar/gkw95528204566PMC5389512PrimaryPrimary publication for the tool.10.1093/nargab/lqz01133575563PMC7671380PrimaryPrimary publication for the heteroplasmy or variance calling option.Nicolas Dierckxsenshttps://orcid.org/0000-0001-8051-6602VerityMapVerityMap 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/btaa44032657355PMC7355294FlexRLA Flexible Model For Record Linkagehttps://github.com/robachowyk/FlexRLflexrlbiotools:flexrl0.1.1Libraryhttp://edamontology.org/topic_3345Data identity and mappingC++RGPL-3.0-or-laterEmergingFree of chargeOpen accesshttps://github.com/robachowyk/FlexRLRepositoryhttps://github.com/robachowyk/FlexRL/issuesIssue trackerhttps://github.com/robachowyk/FlexRL/issuesHelpdeskhttps://github.com/robachowyk/FlexRL/issuesDiscussion forumhttps://github.com/robachowyk/FlexRLSource codehttps://cran.r-project.org/package=FlexRLSoftware packagehttps://rdrr.io/cran/FlexRL/api/API documentationhttps://github.com/robachowyk/FlexRLInstallation instructionsQuick start guideTraining materialUser manual10.1093/jrsssc/qlaf016Primary10.48550/arXiv.2407.06835PreprintKayané Robachhttps://www.amsterdamumc.org/en/research/researchers/kayane-robachhttps://orcid.org/0000-0002-5725-623X05grdyy37PersonPrimary contactMITObimMITObim - mitochondrial baiting and iterative mappinghttps://github.com/chrishah/MITObimMITObimbiotools:MITObimv1.9.1Command-line toolhttp://edamontology.org/topic_3168SequencingPythonPerlMITMaturehttps://groups.google.com/forum/#!forum/mitobim-usersDiscussion forumhttps://github.com/chrishah/MITObim/issuesIssue trackerhttps://github.com/chrishah/mitobimRepositoryhttps://doi.org/10.5281/zenodo.1408102OtherThis is a persistent identifier of version 1.9.1.https://github.com/chrishah/MITObimGeneral10.1093/nar/gkt37123661685PMC3711436PrimaryChristoph Hahnchristoph.hahn@uni-graz.atpathogensurveillancePathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance. The pipeline accepts paths to raw reads for one or more organisms and creates reports in the form of an interactive HTML document. Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed by a more robust multi gene phylogeny and SNP-based phylogeny.https://nf-co.re/pathogensurveillance/pathogensurveillancebiotools:pathogensurveillance1.1.0Command-line toolhttp://edamontology.org/topic_0622GenomicsLinuxGroovyRBashMITEmergingFree of chargeOpen accesshttps://github.com/nf-core/pathogensurveillanceRepositoryhttps://github.com/nf-core/pathogensurveillance/issuesIssue trackerhttps://github.com/nf-core/pathogensurveillance/archive/refs/tags/1.1.0.tar.gzSource code1.1.0https://nf-co.re/pathogensurveillanceUser manualphantasusIt is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.http://bioconductor.org/packages/release/bioc/html/phantasus.htmlphantasusbiotools:phantasus1.0.2Libraryhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3308TranscriptomicsLinuxMacWindowsRMITBioConductorFree of chargehttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_3223Differential gene expression analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_0337Visualisationhttps://alserglab.wustl.edu/phantasusMirrorhttps://github.com/alserglab/phantasus/issuesIssue trackerhttps://github.com/alserglab/phantasus/issuesRepositoryhttp://bioconductor.org/packages/release/bioc/src/contrib/phantasus_1.0.2.tar.gzSoftware packagehttp://bioconductor.org/packages/release/bioc/manuals/phantasus/man/phantasus.pdfUser manualAlexey Sergushichevalsergbox@gmail.comPersonPrimary contactFrameXploreFrameXplore is a Google Colab notebook that extends ColabFold to automatically identify and correct disulfide bonds in cysteine‑rich protein structures. After a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and provides an interactive 3D view.https://github.com/Vidhusv/FRAMEXPLORERframexplorebiotools:framexplore1.0.0doi:10.5281/zenodo.20135079doiWeb applicationhttp://edamontology.org/topic_4019BiosciencesLinuxMacWindowsPythonMITEmergingFree of chargeOpen accesshttps://github.com/Vidhusv/FRAMEXPLORERRepositoryGitHub repository with source code, documentation, and logohttps://github.com/Vidhusv/FRAMEXPLORER/issuesIssue trackerReport bugs, suggest features, or ask questionshttps://github.com/Vidhusv/FRAMEXPLORER/archive/refs/heads/main.zipSource codeLatest version of the complete repository as a ZIP file1.0.0https://raw.githubusercontent.com/Vidhusv/FRAMEXPLORER/main/FrameXplore.ipynbBinariesDirect download of the Colab notebook (.ipynb file). Can be run locally or uploaded to Google Colab.1.0.0https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.mdGeneralQuick start guide, example test case, methodology explanation, citation, and repository contents10.1038/s41592-022-01488-135637307PMC9184281PrimaryColabFold: making protein folding accessible to all. Nature Methods, 2022.Vidhu S Vijayvidhuvijay2003@gmail.comhttps://github.com/Vidhusvhttps://orcid.org/0009-0009-1182-2089PersonDeveloperMaintainerMS Bioinformatics student at Amrita Vishwa Vidyapeetham; creator and maintainer of FrameXplore.paradigmaParadigma is a toolbox for processing and feature extraction from wearable sensor data to identify digital biomarkers specifically tailored for Parkinson’s disease.https://github.com/biomarkersParkinson/paradigmaparadigmabiotools:paradigma1.1.1WorkflowSuitehttp://edamontology.org/topic_3360Biomarkershttp://edamontology.org/topic_3334NeurologyLinuxPythonApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/operation_3937Feature extractionhttp://edamontology.org/data_3275Phenotype namehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_2333Binary formathttp://edamontology.org/format_3464JSONhttps://research-software-directory.org/software/paradigmaSoftware cataloguehttps://github.com/biomarkersParkinson/paradigma/issuesIssue trackerhttps://pypi.org/p/paradigmaSoftware cataloguehttps://biomarkersparkinson.github.io/paradigma/Training materialUser manual10.5281/zenodo.13838392PreprintLightLogRProcess Data from Wearable Light Loggers and Optical Radiation Dosimeters.
Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package for R statistical software implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.https://tscnlab.github.io/LightLogR/lightlogrbiotools:lightlogr0.10.3Libraryhttp://edamontology.org/topic_4010Open sciencehttp://edamontology.org/topic_4019Bioscienceshttp://edamontology.org/topic_3379Preclinical and clinical studiesMacLinuxWindowsRMITMatureFree of chargeOpen accesshttps://github.com/tscnlab/LightLogRRepositoryhttps://lists.lrz.de/mailman/listinfo/lightlogr-usersMailing listhttps://github.com/tscnlab/LightLogR/issuesIssue trackerhttps://cran.r-project.org/package=LightLogRSoftware packagein an R environment run:
install.packages("LightLogR")0.11.3https://tscnlab.github.io/LightLogR/Generalhttps://tscnlab.github.io/LightLogR_webinar/Training material10.21105/joss.0760140123959PMC7617517Johannes Zaunerjohannes.zauner@tum.dehttps://orcid.org/0000-0003-2171-4566PersonMaintainerProteoPyProteoPy is a lightweight Python library for protein- and peptide-level quantitative proteomics analysis, built around the AnnData class as its core data structure. It streamlines data import, preprocessing, and differential analysis while preserving all metadata within a single object.https://proteopy.readthedocs.io/en/latest/proteopybiotools:proteopy0.1.1Libraryhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3520Proteomics experimentWindowsMacLinuxPythonApache-2.0mass spectrometryproteomicsEmergingFree of chargeOpen accesshttps://github.com/UKHD-NP/proteopyRepositoryhttps://github.com/UKHD-NP/proteopy/discussionsDiscussion forumhttps://github.com/UKHD-NP/proteopy/issuesIssue trackerhttps://proteopy.readthedocs.io/en/latest/OtherDocumentationhttps://github.com/UKHD-NP/proteopy/archive/refs/heads/main.zipSource codehttps://proteopy.readthedocs.io/en/latest/Generalanndatauses10.64898/2026.03.31.715273PreprintIsabell Bludauisabell.bludau@med.uni-heidelberg.dehttps://orcid.org/0000-0002-2601-238XPersonPrimary contactJunior Group Leader at the Department of Neuropathology, University Hospital HeidelbergIan Dirk FichtnerIanDirk.Fichtner@med.uni-heidelberg.dehttps://orcid.org/0009-0002-3000-2907PersonDeveloperPhD student at the Department of Neuropathology, University Hospital Heidelberg and Division of Artificial Intelligence in Oncology, German Cancer Research Center (DKFZ)SAMBO OptimizationSequential and model-based optimization for Python with state-of-the-art performance.https://sambo-optimization.github.io/sambo_sequential_model-based_optimizationbiotools:sambo_sequential_model-based_optimizationv1.25.2Libraryhttp://edamontology.org/topic_3569Applied mathematicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3474Machine learningAGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_2425Optimisation and refinementhttps://github.com/sambo-optimization/samboRepositoryhttps://github.com/sambo-optimization/sambo/issuesIssue trackerhttps://sambo-optimization.github.io/doc/sambo/API documentation10.5281/zenodo.14461363RosalutionRosalution assists researchers study genetic variation 🧬 in patients 🧑🏾🤝🧑🏼 by helping select candidate animal models 🐀🐁🐠🪱 to replicate the variation to further research to derive, diagnose, and provide therapies for ultra-rare diseases. Developed by the UAB Center for Computational Genomics and Data Science (CGDS).https://github.com/uab-cgds-worthey/rosalutionrosalutionbiotools:rosalution0.8.8-erWeb applicationhttp://edamontology.org/topic_0199Genetic variationJavaScriptPythonGPL-3.0Rare DiseaseMatureFree of chargehttps://github.com/uab-cgds-worthey/rosalutionRepositoryhttps://github.com/uab-cgds-worthey/rosalution/issuesIssue trackerhttps://github.com/uab-cgds-worthey/rosalution/releases/tag/0.8.8-erSource code0.8.8-er10.21105/joss.05443Angelina Uno-Antonisonhttps://github.com/SeriousHorncatbio.toolsThe community registry of computational tools and data resources for biosciences.https://bio.toolsbio.toolsbiotools:bio.toolsRRID:SCR_014695rridWeb APIDatabase portalWeb applicationhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3307Computational biologyJavaScriptPythonGPL-3.0EmergingFree of chargeOpen accessToolsDenmarkhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_3671Texthttp://edamontology.org/format_1964plain text format (unformatted)https://biotools.readthedocs.io/en/latest/support.html?highlight=helpHelpdeskhttps://github.com/bio-tools/biotoolsregistry/issuesIssue trackerhttps://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-listMailing listhttps://github.com/bio-tools/biotoolsregistry/Repositoryhttps://github.com/bio-tools/biotoolsRegistrySource codehttps://biotools.readthedocs.io/en/latest/api_usage_guide.htmlAPI documentationAPI usage guidehttps://biotools.readthedocs.io/en/latest/api_reference.htmlAPI documentationAPI Referencehttps://biotools.readthedocs.io/en/latest/publications.html#citationCitation instructionshttps://biotools.readthedocs.io/en/latest/contributors_guide.htmlContributions policyhttps://biotools.readthedocs.io/en/latest/Generalhttps://biotools.readthedocs.io/en/latest/governance.htmlGovernancehttps://biotools.readthedocs.io/en/latest/curators_guide.htmlUser manualCurators Guide10.1093/nar/gkv1116Primary10.12688/f1000research.12974.1Other10.1093/gigascience/gix022Other10.1007/s10009-015-0392-zOtherContributorshttps://biotools.readthedocs.io/en/latest/contributors.htmlPersonThe MINERVA PlatformThe MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource.
The MINERVA Platform is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using React.js. The displayed content is visualized by OpenLayers API, dedicated JavaScript and CSS.https://minerva.uni.luMINERVA_Platformbiotools:MINERVA_Platform13.1.313.2.014.0.1315.0.316.4.017.1.318.1.119.1.019.1.320.0.3http://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3391Omicshttp://edamontology.org/topic_3342Translational medicinehttp://edamontology.org/topic_2259Systems biologyAGPL-3.0LCSBELIXIR-LUMatureFree of chargeOpen accessToolsLuxembourghttp://edamontology.org/operation_3926Pathway visualisationVisualise systems biology diagrams online, on a standalone web serverhttp://edamontology.org/operation_0571Expression data visualisationVisualise omics data from multiple datasets on top of the diagramshttp://edamontology.org/operation_3434ConversionConvert between main systems biology layout formats: CellDeslgners SBML, SBML layout+render, SBGN-ML, GPMLhttp://edamontology.org/operation_2426Modelling and simulationUse MINERVA API to access systems biology formats for modellinghttps://gitlab.lcsb.uni.lu/minerva/core/RepositoryGiLab repository for core functionalities (data and format handling, service stability, API access)https://gitlab.lcsb.uni.lu/minerva/core/-/issuesIssue trackerIssue tracker for core functionalities (data and format handling, service stability, API access)https://gitlab.lcsb.uni.lu/minerva/frontendRepositoryGiLab repository for frontend functionalitieshttps://gitlab.lcsb.uni.lu/minerva/frontend/-/issuesIssue trackerIssue tracker for frontend functionalitieshttps://minerva.pages.uni.lu/doc/install/OtherInstallation instructions, including debian package, virtual machine images and docker containers.13.1.3 - 20.0.3https://minerva.uni.luQuick start guideRelease notesUser manualAPI documentationCitation instructionsTerms of usepathvisiousessbgnuseslibsbmluses10.1038/npjsba.2016.2028725475PMC5516855Primary10.010.1093/bioinformatics/btz28631074494PMC6821317Primary12.2.310.1093/bib/bbz06731273380PMC7373180Primary13.1.110.1089/big.2015.005727441714PMC4932659Usage10.010.1016/j.envpol.2019.04.0053099127913.1.1Marek Ostaszewskihttps://orcid.org/0000-0003-1473-370XPersonPrimary contactPiotr Gawronhttps://orcid.org/0000-0002-9328-8052PersonDeveloperReinhard Schneiderhttps://orcid.org/0000-0002-8278-1618PersonProviderVenkata Satagopamhttps://orcid.org/0000-0002-6532-5880PersonSupportRudi Ballinghttps://orcid.org/0000-0003-2902-5650PersonProviderDavid Hokszahttps://orcid.org/0000-0003-4679-0557PersonContributorEwa Smulahttps://orcid.org/0000-0001-7118-3164PersonMaintainerCOPASIOpen-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. It includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.http://copasi.org/copasibiotools:copasiCommand-line toolLibraryDesktop applicationhttp://edamontology.org/topic_2259Systems biologyMacLinuxWindowsC++Artistic-2.0de.NBIEBI Training ToolsMatureFree of chargeOpen accessGermanyhttp://edamontology.org/operation_3562Network simulationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3926Pathway visualisationhttp://edamontology.org/operation_3660Metabolic network modellinghttp://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3686COMBINE OMEXhttp://edamontology.org/format_3685SED-MLhttp://edamontology.org/format_3239CopasiMLhttp://edamontology.org/format_2585SBMLhttps://groups.google.com/g/copasi-user-forumDiscussion forumUser Forumhttp://tracker.copasi.org/Issue trackerIssue trackerhttps://github.com/copasi/COPASIRepositoryGithub Repohttps://fosstodon.org/@copasiSocial mediahttp://copasi.org/Download/BinariesSource and binary packages are available for download.http://copasi.org/Support/User_Manual/User manualcorcusedBypycotoolsusedBybiosimulationsincludedInsbmlwebappusedBylibsbmlusesbasicousedBy10.1093/bioinformatics/btl4851703268310.1007/978-1-59745-525-1_21939943310.1016/j.jbiotec.2017.06.120028655634PMC5623632http://copasi.org/About/Team/PersonPrimary contactFrank T. Bergmannfrank.bergmann@bioquant.uni-heidelberg.dehttps://orcid.org/0000-0001-5553-4702PersonPrimary contactBCFtoolsBCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.http://www.htslib.org/bcftoolsbiotools:bcftools1.01.11.21.31.3.11.41.4.11.51.61.71.81.91.101.10.11.10.21.111.121.131.141.151.15.11.161.171.181.191.201.211.21.11.221.22.11.231.23.1SuiteCommand-line toolhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_3516Genotyping experimentMacLinuxWindowsCMITBCFtoolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3020BCFhttp://edamontology.org/format_3016VCFMultiple data munging operations.https://github.com/samtools/bcftoolsRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/bcftools/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/bcftools.htmlGeneralhttp://www.htslib.org/workflow/#mapping_to_variantOtherA workflow for BCFtools.htslibuses10.1093/bioinformatics/btp35219505943PMC2723002PrimaryThe Sequence Alignment/Map format and SAMtools.10.1093/gigascience/giab00833590861PMC7931819PrimaryTwelve years of SAMtools and BCFtools.Wellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportSAMtoolsSAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.http://www.htslib.org/samtoolsbiotools:samtools1.01.11.21.31.3.11.41.4.11.51.61.71.81.91.101.111.121.131.141.151.15.11.161.16.11.171.181.191.19.11.19.21.201.211.21.11.221.22.11.22.21.231.23.1SuiteCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3325Rare diseasesMacLinuxWindowsCMITAnimal and Crop GenomicsRare DiseaseSAMtoolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_3096Data editinghttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/operation_3802Data sortinghttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_2573SAMhttps://github.com/samtools/samtoolsRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/samtools/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/#howtosOtherHowTos for samtoolshttp://www.htslib.org/doc/#manual-pagesUser manualhttp://www.htslib.org/download/Installation instructionshtslibuses10.1093/bioinformatics/btp35219505943PMC2723002PrimaryThe Sequence Alignment/Map format and SAMtools.10.1093/gigascience/giab00833590861PMC7931819PrimaryTwelve years of SAMtools and BCFtools.10.1093/bioinformatics/btr50921903627PMC3198575Richard Durbinrd@sanger.ac.ukPersonContributorWellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderPrimary contactSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportHTSlibThe main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.http://www.htslib.org/htslibbiotools:htslib1.01.11.21.2.11.31.3.11.3.21.41.4.11.51.61.71.81.91.101.10.11.10.21.111.121.131.141.151.15.11.161.171.181.191.201.21.11.221.22.11.22.21.231.23.1Libraryhttp://edamontology.org/topic_3071Data managementWindowsLinuxMacCMITAnimal and Crop GenomicsMatureFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3020BCFhttp://edamontology.org/format_3016VCFhttps://github.com/samtools/htslibRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/htslib/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/#manual-pagesUser manualsamtoolsusedBybcftoolsusedBy10.1093/gigascience/giab00733594436PMC7931820PrimaryHTSlib: C library for reading/writing high-throughput sequencing data.Wellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderPrimary contactSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportRhizoVision ExplorerRhizoVision Explorer is free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera. Root images are expected to have a high contrast of roots with the background, homogenous lighting, and minimal overlapping of roots.https://github.com/noble-research-institute/RhizoVisionExplorerrhizovision-explorerbiotools:rhizovision-explorerDesktop applicationhttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3298PhenomicsC++GPL-3.0http://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3937Feature extractionhttps://github.com/rootphenomicslab/RhizoVisionExplorer/issuesIssue tracker10.1093/aobpla/plab05634804466PMC8598384PrimaryLarry M. Yorklmyork@noble.orghttps://orcid.org/0000-0002-1995-9479PersonPrimary contactQUASTQUAST 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 contactWEBnmaWEBnm@ provides quick, automated computation and analysis of low-frequency normal modes for protein structures.http://apps.cbu.uib.no/webnmawebnmabiotools:webnma3.5Web APISuitehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacPythonGPL-3.0BiB toolsCBU toolsUiB toolsELIXIR-NOELIXIR-NorwayMatureFree of chargeOpen access3D-BioInfoNorwayhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBConstructs elastic network model from alpha carbon coordinates of the protein, and computes properties to describe large scale conformations. Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plotshttp://edamontology.org/operation_2487Protein structure comparisonhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBPerforms comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plotshttps://github.com/reuter-group/webnma3RepositoryIssue trackerhttps://elixir.no/helpdeskHelpdeskHelpdesk and support for ELIXIR Norway services.http://apps.cbu.uib.no/webnma3/howto/singleQuick start guidehttp://apps.cbu.uib.no/webnma3/qandaFAQhttp://apps.cbu.uib.no/webnma3/aboutGeneralCitation instructionsnumpyusesbiopythonusesmatplotlibusesmustangusesdsspuses10.1186/s12859-014-0427-625547242PMC4339738Primary2.010.1186/1471-2105-6-5215762993PMC1274249Primary1.0Nathalie ReuterNathalie.Reuter@uib.nohttp://www.cbu.uib.no/reuter/https://orcid.org/0000-0002-3649-7675PersonPrimary contactDeveloperSandhya P Tiwarihttps://orcid.org/0000-0002-0747-3826PersonDeveloperKidane M TeklePersonDeveloperTristan CragnoliniPersonDeveloperSvenn H GrindhaugPersonDeveloperLars SkjærvenPersonDeveloperGisle SalensmindePersonDeveloperEdvin FuglebakkPersonDeveloperSiv M HollupPersonDeveloperDepartment of Molecular Biology, University of Bergen, NorwayInstituteProviderComputational Biology Unit, Department of Informatics, University of Bergen, NorwayInstituteProviderUiBInstituteProviderCNPS.cycleCNPS.cycle is an R package designed to streamline the analysis of shotgun metagenomic data related to biogeochemical cycles, providing users with visually informative outputs and automating key steps in data processing and analysis.https://github.com/yuezhengfu/CNPS.cycle/wikicnpscyclebiotools:cnpscyclehttp://edamontology.org/topic_4020Carbon cyclehttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3837Metagenomic sequencinghttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_3697Microbial ecologyRhttp://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_3891Essential dynamicshttps://github.com/yuezhengfu/CNPS.cycle/issuesIssue tracker10.1128/MSYSTEMS.01021-2541123363PMC12625701Jing Zhangjingjing_friends@hotmail.comhttps://orcid.org/0000-0001-5569-7763PersonYukun Zouyukun.zou@catas.cnhttps://orcid.org/0000-0003-3622-9328PersonMEAanalysisMEAanalysis is an open-source R package for visualizing burst parameters at the single-electrode level from AxIS Navigator MEA data, facilitating reproducible analysis and comparison of bursting parameters.https://egordon2.github.io/MEA-analysis-package/meaanalysisbiotools:meaanalysishttp://edamontology.org/topic_3300Physiologyhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0769WorkflowsRGPL-2.0http://edamontology.org/operation_0337Visualisationhttps://github.com/egordon2/MEA-analysis-package/issuesIssue tracker10.1093/BIOADV/VBAF16040746508PMC12311347Emily A Gordonemily.gordon@wadham.ox.ac.ukhttps://orcid.org/0009-0004-9490-5990PersonRQdeltaCTRQdeltaCT is an R package designed for relative quantification of gene expression using delta Ct methods. It provides tools for data import, quality control, visualization, and statistical analysis of real-time PCR data, catering to both beginners and experienced R users.https://CRAN.R-project.org/package=RQdeltaCTrqdeltactbiotools:rqdeltacthttp://edamontology.org/topic_3452Tomographyhttp://edamontology.org/topic_3519PCR experimenthttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0632Probes and primersRGPL-3.0http://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_2940Scatter plot plottinghttps://github.com/Donadelnal/RQdeltaCT/issues/1Issue tracker10.1038/S41598-025-11822-040804269PMC12350606Daniel Zalewskidaniel.zalewski@umlub.plPersoneyeriseyeris is an R framework designed for flexible, extensible, and reproducible pupillometry preprocessing. It provides a complete workflow and addresses the need for standardized and FAIR data handling in pupillometry research.https://shawnschwartz.com/eyeris/reference/zscore.htmleyerisbiotools:eyerishttp://edamontology.org/topic_4014Electroencephalographyhttp://edamontology.org/topic_4012FAIR datahttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0769WorkflowsPythonMIThttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3359Splittinghttps://shawnschwartz.com/eyerisOtherhttps://cran.r-project.org/package=eyerisRepositoryhttps://github.com/shawntz/eyeris/issuesIssue tracker10.1101/2025.06.01.657312Shawn T SchwartzPersonPlantCVPlantCV is a free and open-source package used for image analysis of plant phenotypes. It offers a pipeline for capturing, labeling, and transferring plant images, enabling quantification of traits such as plant size, height, and color.https://plantcv.readthedocs.io/en/latest/plantcvbiotools:plantcvhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3300Physiologyhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3443Image analysishttps://github.com/danforthcenter/plantcv/issuesIssue tracker10.3791/6761940228008Katherine M MurphyKMurphy@danforthcenter.orghttps://orcid.org/0000-0002-8891-4274PersonSeroBA(v2.0)SeroBA(v2.0) is a tool and atlas designed to accurately identify pneumococcal serotypes based on genome sequencing. It provides a comprehensive library of known serotypes and incorporates a community-contribution system for updates.https://www.pneumogen.net/gps/#/serobankserobankbiotools:serobankhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_2830Immunoproteins and antigenshttp://edamontology.org/operation_0496Global alignmenthttps://github.com/GlobalPneumoSeq/seroba/issuesIssue tracker10.1101/2025.04.16.648953mdciaomdciao is an open-source command-line tool and Python API for analyzing and visualizing molecular dynamics (MD) simulation data, particularly focused on residue-residue contact frequencies and enriched with domain-specific annotations.https://www.mdciao.orgmdciaobiotools:mdciaohttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0092Data visualisationPythonLGPL-3.0http://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0337Visualisationhttps://pypi.org/project/mdciao/Repositoryhttps://github.com/gph82/mdciao/issuesIssue trackerhttps://proteinformatics.uni-leipzig.de/mdciao/overview.htmlGeneralhttps://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examplesTraining material10.1371/JOURNAL.PCBI.101283740258031PMC12011235Guillermo Pérez-Hernándezguillermo.perez@charite.dehttps://orcid.org/0000-0002-9287-8704PersonPASTAQPASTAQ (Pipelines And Systems for Threshold Avoiding Quantification) provides a set of tools for high-performance pre-processing of LC-MS/MS data. Avoiding the use of arbitrary intensity thresholds in early stages of the pipeline can aid in the detection of important biological low intensity signals common in metabolomics and proteomics experiments.https://pastaq.horvatovichlab.compastaqbiotools:pastaqWorkflowLibraryhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0154Small moleculesC++PythonMIThttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3215Peak detectionhttps://github.com/PASTAQ-MS/PASTAQRepositoryhttps://github.com/PASTAQ-MS/PASTAQ/issuesIssue tracker10.1021/acs.analchem.1c0189234355890PMC8374884PrimaryPeter Horvatovichp.l.horvatovich@rug.nlhttps://orcid.org/0000-0003-2218-1140PersonPrimary contactBridgeDbBridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.http://bridgedb.github.io/bridgedbbiotools:bridgedb3.0.18Libraryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_2840ToxicologyMacLinuxWindowsJavaApache-2.0ProteomicsELIXIR-NLBIGCAT-UMBridgeDbRare DiseaseMatureFree of chargeInteroperabilityNetherlandshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1025Gene identifierAPI for converting gene identifiers (Ensembl, Entrez) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0989Protein identifierhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1086Compound identifierAPI for converting compound identifiers (HMDB, ChEBI, ChemSpider, PubChem, etc) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.https://github.com/bridgedb/BridgeDbRepositoryhttps://github.com/bridgedb/BridgeDb/issuesIssue trackerhttps://fosstodon.org/@bridgedbSocial mediahttps://bridgedb.github.io/pages/docs.htmlGeneralidentifiers.orgusesbioregistryuses10.1186/1471-2105-11-520047655PMC282467810.1007/978-3-319-11964-9_7Primary10.3897/rio.8.e83031PrimaryMaastricht UniversityInstituteProviderrWikiPathwaysUse this package to interface with the WikiPathways API.http://bioconductor.org/packages/release/bioc/html/rWikiPathways.htmlrwikipathwaysbiotools:rwikipathways1.0.01.26.0Libraryhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0091BioinformaticsWindowsMacLinuxRMITRare DiseaseBioConductorCOVID-19Free of chargeMetabolomicsNetherlandshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_3952Pathway ID (WikiPathways)https://github.com/wikipathways/rwikipathwaysMirrorhttps://github.com/wikipathways/rwikipathways/issuesIssue trackerhttp://bioconductor.org/packages/release/bioc/src/contrib/rWikiPathways_1.0.0.tar.gzDownloads pagehttp://bioconductor.org/packages/release/bioc/manuals/rWikiPathways/man/rWikiPathways.pdfUser manualbridgedbrusedBywikipathwaysuses10.1093/nar/gkx106429136241PMC5753270Primary10.1093/nar/gkad96037941138PMC10767877Primary10.1093/nar/gkaa102433211851PMC7779061PrimaryEgon Willighagenegon.willighagen@gmail.comhttps://orcid.org/0000-0001-7542-028602jz4aj89PersonPrimary contactAlexander Picoalex.pico@gladstone.ucsf.eduhttps://orcid.org/0000-0001-5706-2163PersonPrimary contactDenise Slenterhttps://orcid.org/0000-0001-8449-131802jz4aj89PersonMartina Kutmonhttps://orcid.org/0000-0002-7699-819102jz4aj89PersonSusan Coorthttps://orcid.org/0000-0003-1224-969002jz4aj89PersonMarvin Martenshttps://orcid.org/0000-0003-2230-084002jz4aj89PersonmetabuliMetabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acidhttps://metabuli.steineggerlab.commetabulibiotools:metabuliCommand-line toolDesktop applicationhttp://edamontology.org/topic_0637TaxonomyWindowsMacLinuxC++GPL-3.0MatureFree of chargehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/steineggerlab/Metabuli/issuesIssue trackerhttps://github.com/steineggerlab/MetabuliRepositorygithub repositorymmseqs2usesgtdbuses10.1038/s41592-024-02273-y38769467decompTumor2SigR package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.http://rmpiro.net/decompTumor2Sig/decompTumor2Sigbiotools:decompTumor2Sig2.0.0Libraryhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacRGPL-2.0MatureFree of chargehttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_1812Parsinghttps://github.com/rmpiro/decompTumor2Sig/issuesIssue trackerhttps://github.com/rmpiro/decompTumor2SigRepositoryhttps://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.htmlSoftware cataloguehttp://rmpiro.net/index.html#downloadsDownloads pagehttps://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdfUser manual10.1186/s12859-019-2688-630999866PMC6472187PrimaryProf. Dr. Rosario M. Piror.piro@fu-berlin.dePersonPrimary contactDeveloperpantasDifferential quantification of alternative splicing events on spliced pangenome graphs.https://github.com/algolab/pantaspantasbiotools:pantasCommand-line toolhttp://edamontology.org/topic_3320RNA splicingLinuxGPL-3.0Open accessToolsItalyhttps://github.com/AlgoLab/pantasRepositoryhttps://github.com/AlgoLab/pantas/issuesIssue trackerhttps://github.com/AlgoLab/pantasSource codehttps://hub.docker.com/r/algolab/pantasContainer filehttps://github.com/AlgoLab/pantas/blob/main/README.mdGeneralInstallation instructionsQuick start guideCommand-line options10.1371/journal.pcbi.1012665PrimaryRecGraphRecGraph is a tool for computing optimal sequence-to-graph alignment with recombinations.https://github.com/AlgoLab/RecGraphrecgraphbiotools:recgraph1.0.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3796Population genomicsLinuxMacRustMITEmergingToolsItalyhttps://github.com/AlgoLab/RecGraphRepositoryhttps://github.com/AlgoLab/RecGraph/issuesIssue trackerhttps://github.com/AlgoLab/RecGraph/releases/tag/v1.0.0Binaries1.0.0https://anaconda.org/channels/bioconda/packages/recgraph/overviewSoftware packagehttps://github.com/AlgoLab/RecGraph/blob/main/README.mdGeneral10.1093/bioinformatics/btae292Primary1.0.0BaktaRapid & standardized annotation of bacterial genomes, MAGs & plasmidshttps://github.com/oschwengers/baktabaktabiotools:baktav1.12.0Web applicationCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0091BioinformaticsLinuxMacPythonGPL-3.0MatureFree of chargeOpen accessToolsGermanyhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2914Sequence features metadatahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_1975GFF3http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/format_3329HMMER3bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fastahttps://github.com/oschwengers/baktaRepositoryhttps://github.com/oschwengers/bakta/issuesIssue trackerhttps://bioconda.github.io/recipes/bakta/README.htmlOtherhttps://bakta.computational.bioServicehttps://zenodo.org/records/14916843OtherMandatory annotation databasev6.0https://github.com/oschwengers/bakta/blob/main/README.mdGeneralhttps://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.mdContributions policyhttps://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.mdCode of conducthttps://bakta.readthedocs.io/User manualdiamonduseshmmer3usesinfernalusestrnascan-seusesblastusesaragornusespilercrusesdeepsiguses10.1099/mgen.0.00068534739369PMC8743544Primary1.110.1093/nar/gkaf33540271661PMC12230652PrimaryOliver Schwengersoliver.schwengers@cb.jlug.dehttps://github.com/oschwengershttps://orcid.org/0000-0003-4216-2721PersonPrimary contactDeveloperMaintainerJustus Liebig University Giessenhttps://www.uni-giessen.deInstituteProvideriCodoniCodon is a tool for ideal codon design for customized gene expression.https://bazzinilab.shinyapps.io/icodon/icodonbiotools:icodonWeb applicationLibraryhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNARhttp://edamontology.org/operation_3095Nucleic acid designhttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_0441cis-regulatory element predictionhttps://github.com/santiago1234/iCodonRepositoryhttps://github.com/santiago1234/iCodon/issuesIssue tracker10.1101/2021.05.06.442969PrimaryAriel Alejandro Bazziniarb@stowers.orgPersonPrimary contactkraken2Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.
Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”)https://github.com/DerrickWood/kraken2kraken2biotools:kraken22.0.8-betaCommand-line toolhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3301MicrobiologyPerlC++MITONTeaterFree of chargeOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA`kraken2 --db <kraken2_database> <input.fastq>`https://github.com/DerrickWood/kraken2Repositoryhttps://github.com/DerrickWood/kraken2/issuesIssue trackerhttps://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gzSource code2.0.8-betahttps://github.com/DerrickWood/kraken2/wiki/ManualUser manualhttps://benlangmead.github.io/aws-indexes/k2User manualLinks to multiple Kraken 2 and bracken databases and indexeskrakenisNewVersionOfbrackenusedBygtdbuses10.1101/762302Derrick E. Woodhttp://orcid.org/0000-0002-7429-1854PersonJennifer Luhttp://orcid.org/0000-0001-9167-2002PersonBen Langmeadlangmea@cs.jhu.eduhttp://orcid.org/0000-0003-2437-1976PersonDOME RegistryA database of annotations for published papers describing machine learning methods in biology.https://registry.dome-ml.org/dome_registrybiotools:dome_registry1.0Database portalWeb applicationhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_4019Bioscienceshttp://edamontology.org/topic_3316Computer scienceCC-BY-NC-4.0MatureFree of chargeOpen accessDataIntrinsically Disordered ProteinsItalyGreecehttps://github.com/BioComputingUP/dome-registry/issuesIssue trackerhttps://github.com/BioComputingUP/dome-registryInstallation instructionseuropepmcuseseuropepmcusedBy10.1093/gigascience/giae09439661723PMC11633452Gavin Farrellgavinmichael.farrell@phd.unipd.ithttps://orcid.org/0000-0001-5166-8551PersonSupportCuration and data supportOmar Attafiomarabdelghani.attafi@studenti.unipd.ithttps://orcid.org/0009-0002-2327-9430pyXLMSpyXLMS is a python package and web application with graphical user interface that aims to simplify and streamline the intermediate step of connecting crosslink search engine results with down-stream analysis tools, enabling researchers even without bioinformatics knowledge to conduct in-depth crosslink analyses and shifting the focus from data transformation to data interpretation and therefore gaining biological insight.https://github.com/hgb-bin-proteomics/pyXLMSpyxlmsbiotools:pyxlms1.7.5+LibraryWeb applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0128Protein interactionsLinuxMacWindowsPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3475TSVhttps://github.com/hgb-bin-proteomics/pyXLMSRepositoryhttps://github.com/hgb-bin-proteomics/pyXLMS/issuesIssue trackerhttps://hgb-bin-proteomics.github.io/pyXLMS/OtherAPI Documentationhttps://hgb-bin-proteomics.github.io/pyXLMS-docsOtherUser Guidehttps://hgb-bin-proteomics.github.io/pyXLMS-appServicehttps://pypi.org/project/pyXLMS/Software packagehttps://github.com/hgb-bin-proteomics/pyXLMSSource codehttps://hgb-bin-proteomics.github.io/pyXLMS/API specificationhttps://hub.docker.com/r/michabirklbauer/pyxlmsContainer filehttps://hgb-bin-proteomics.github.io/pyXLMS-appTool wrapper (Other)https://hgb-bin-proteomics.github.io/pyXLMS/API documentationhttps://hgb-bin-proteomics.github.io/pyXLMS-docsUser manualhttps://github.com/hgb-bin-proteomics/pyXLMS/blob/master/CODE_OF_CONDUCT.mdCode of conducthttps://github.com/hgb-bin-proteomics/pyXLMS/blob/master/CONTRIBUTING.mdContributions policyhttps://github.com/hgb-bin-proteomics/pyXLMS/releasesRelease notesms_annikausesmaxquantusesmeroxusesplink-2usespyteomicsusesbiopythonuses10.64898/2025.12.18.695169PreprintMicha Johannes Birklbauermicha.birklbauer@fh-hagenberg.athttps://orcid.org/0009-0005-1051-179XPersonMaintainerViktoria Dorferviktoria.dorfer@fh-hagenberg.athttps://orcid.org/0000-0002-5332-5701PersonContributorProteomics FHOÖ Campus Hagenbergproteomics@fh-hagenberg.atDivisionPrimary contactMicrobiomeRMicrobiomeR is an R package for microbiome analysis that incorporates phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows.https://vallenderlab.github.io/MicrobiomeR/MicrobiomeRbiotools:MicrobiomeR0.6.1Libraryhttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3174MetagenomicsWindowsLinuxRMITFree of chargehttps://github.com/vallenderlab/MicrobiomeR/issuesIssue trackerhttps://github.com/vallenderlab/MicrobiomeRRepositoryhttps://github.com/vallenderlab/MicrobiomeR/releases/download/v0.6.1/MicrobiomeR_0.6.1.tar.gzSoftware package0.6.1https://microbiomer.vallenderlab.science/General10.21105/joss.01299PrimaryRobert Gilmorergilmore@umc.eduhttp://orcid.org/0000-0001-8096-0180PersonPrimary contactShaurita D. Hutchinsshutchins2@umc.eduhttp://orcid.org/0000-0002-7687-0059PersonDeveloperEasyPubPlotEasyPubPlot is a Shiny web application and associated R package designed for rapid omics data exploration and visualization. It simplifies the creation of publishable plots like scores plots, volcano plots, and heatmaps, guiding users through the process with minimal steps.https://pharmaco-omicslab.shinyapps.io/EasyPubPloteasypubplotbiotools:easypubplothttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3168SequencingRhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_2943Box-Whisker plot plottinghttp://edamontology.org/operation_0490Dot plot plottinghttp://edamontology.org/operation_2939Principal component visualisationhttps://github.com/Pharmaco-OmicsLab/EasyPubPlot/issuesIssue tracker10.1101/2024.11.26.625339LimelightLimelight is an open-source, web-based tool for analyzing, visualizing, and sharing mass spectrometry proteomics data. It supports various data formats from common search engines and enables collaborative interpretation of results.https://limelight-ms.org/limelightbiotools:limelighthttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_2949Protein-protein interaction analysishttps://github.com/yeastrc/limelight-core/issuesIssue trackerhttps://limelight.yeastrc.org/limelight/p/demoTraining materialhttps://limelight-ms.readthedocs.io/User manual10.1101/2024.11.01.621597SpliceAI PangolinSpliceAI Pangolin is a web service that predicts the impact of genetic variants on RNA splicing using SpliceAI and Pangolin models. It helps diagnose variants affecting splicing in diseases like Alagille syndrome.https://spliceailookup.broadinstitute.org/spliceaibiotools:spliceaihttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_0433Splice site predictionhttps://github.com/broadinstitute/SpliceAI-lookup/issuesIssue tracker10.1016/J.XHGG.2024.10035139244638PMC1144034510.1101/GR.279158.12439271294PMC11610570Melissa A. Gilbertgilbertma@chop.eduPersonMary-Claire Kingmcking@uw.eduhttps://orcid.org/0000-0001-9426-1743PersonGeoToxGeoTox is an open-source R software package for characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures. It facilitates source-to-outcome continuum modeling for individual and population-level risk assessment.https://niehs.github.io/GeoTox/geotoxbiotools:geotoxhttp://edamontology.org/topic_2840Toxicologyhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3360BiomarkersRhttps://github.com/NIEHS/GeoTox/issuesIssue tracker10.1101/2024.09.23.24314096Kyle P MessierPersonWinnowA confidence rescoring and FDR estimation workflow for de novo peptide sequencing.https://github.com/instadeepai/winnowwinnowbiotools:winnow1.0.3Command-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3474Machine learningLinuxPythonApache-2.0proteomicsProteomicsEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3644de Novo sequencinghttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3651MGFhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3752CSVwinnow predict --data-source instanovo --dataset-config-path test_config.yaml --method winnow --fdr-threshold 0.01 --confidence-column confidence --output-folder ./predictionshttps://github.com/instadeepai/winnowRepositoryhttps://github.com/instadeepai/winnow/issuesIssue trackerhttps://github.com/instadeepai/winnow/archive/refs/tags/v1.0.3.zipSource code1.0.3https://instadeepai.github.io/winnow/api/datasets/API documentationhttps://instadeepai.github.io/winnow/cli/Command-line optionshttps://instadeepai.github.io/winnow/contributing/Contributions policyhttps://instadeepai.github.io/winnow/#bibtex-entry-and-citation-infoCitation instructionshttps://instadeepai.github.io/winnow/#installationInstallation instructionsinstanovouses10.48550/arXiv.2509.24952Primary2Jemma Danielj.daniel@instadeep.comhttps://orcid.org/0000-0002-1964-3976PersonDeveloperDocumentorMaintainerAmandla Mabonahttps://orcid.org/0009-0009-7514-677XDeveloperJeroen van Goeyj.vangoey@instadeep.comhttps://orcid.org/0000-0003-4480-5567Primary contactMaintainerKonstantinos Kalogeropouloskonka@dtu.dkhttps://orcid.org/0000-0003-3907-9281Primary contactContributorthafthaf is a command-line tool to extract transcript sequences from a genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene mapping files compatible with tools such as Salmon.https://crates.io/crates/thafthafbiotools:thaf0.0.4Command-line toolhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3170RNA-SeqMacLinuxWindowsRustBSD-3-ClauseEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3267Sequence coordinate conversionhttp://edamontology.org/data_3494DNA sequenceProduce transcriptome file from genomic DNA and gff3thaf \
-f <INPUT_GFF3> \
-d <DNA_FASTA> \
-t <OUTPUT_FASTA> \
[-g <GENEMAP_FILE>]
[-e <FEATURES>]https://crates.io/crates/thafSoftware catalogueCrates.io page providing installation instructions and README.https://github.com/bourumir-wyngs/thafRepositorySource code. Also, use GitHub issue tracker to send bug reports and extension proposals.https://verdanta.tech/open-source/OtherVerdanta page for thafhttps://crates.io/crates/thafOtherUse Cargo commands to install the application. Cargo will build it from the source.0.0.4https://crates.io/crates/thafGeneralREADME provides enough information to use the toolAudrius Meskauskascontact@verdanta.techhttps://verdanta.infohttps://orcid.org/0009-0006-1714-3691PersonVerdanta is an early startup in Switzerland, providing curated RNASeq pipeline. Thaf is part of our software stack that is released open source.JalviewJalview 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/0000-0002-9014-5355