ancseqA local command-line tool for ancestral sequence reconstruction with gap-state inference using IQ-TREE. It supports nucleotide, amino acid, and codon sequence alignments and reports site-wise posterior probabilities of ancestral states.https://github.com/YuSugihara/ancseqancseqbiotools:ancseqCommand-line toolhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3945Molecular evolutionPythonGPL-3.0-or-laterMatureFree of chargehttp://edamontology.org/operation_3745Ancestral reconstructionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTAReconstructs ancestral nucleotide, amino acid, or codon sequences, including ancestral gap states, and reports site-wise posterior probabilities.https://github.com/YuSugihara/ancseqRepositoryhttps://github.com/YuSugihara/ancseq/issuesIssue trackerReport bugs or request new features.https://github.com/YuSugihara/ancseq/releasesDownloads pagehttps://github.com/YuSugihara/ancseq#readmeCitation instructionsCommand-line optionsInstallation instructionsUser manualiqtreeuses10.1371/journal.pgen.101165340202957PMC11981194PrimaryUsage1.2.1ancseq was developed and used to reconstruct ancestral NRC3 sequences in this study.10.64898/2025.12.17.694876Usageancseq was used to reconstruct ancestral RAR1 and SGT1 sequences in this study.Yu Sugiharahttps://yusugihara.github.io/https://orcid.org/0000-0001-6042-1091PersonPrimary contactDeveloperMaintainerRiSPICERiSPICE (Rice SNP Prioritization Integrating Chromatin Effects) is a computational framework for prioritizing non-coding rice variants by integrating predicted chromatin effects from a fine-tuned DNA language model.https://github.com/bioinfodlsu/rispicerispicebiotools:rispiceWorkflowhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_3173Epigenomicshttp://edamontology.org/topic_3517GWAS studyLinuxPythonMIThttps://github.com/bioinfodlsu/rispiceRepositoryRiSPICE GitHub Repositoryhttps://huggingface.co/paolomanlapaz/rispice-baseRepositoryRiSPICE Base Model to be used alongside the LoRA Adapters.https://huggingface.co/paolomanlapaz/rispice-1000bpRepositoryLoRA Adapter for 1000bp RiSPICE in HuggingFacehttps://huggingface.co/paolomanlapaz/rispice-750bpRepositoryLoRA Adapter for 750bp RiSPICE in HuggingFacehttps://huggingface.co/paolomanlapaz/rispice-500bpRepositoryLoRA Adapter for 500bp RiSPICE in HuggingFaceJosef Paolo Manlapazjosef.paolo.manlapaz@gmail.comhttps://orcid.org/0009-0000-5541-9384PersonContributorAnish M.S. Shresthaanish.shrestha@dlsu.edu.phhttps://orcid.org/0000-0002-9192-9709PersonContributorREFUTEREFUTE is an open benchmark for scientific critique honesty and epistemic calibration on recent life-science and biomedical literature. It tests whether models keep claims inside what the evidence allows (overclaim / planted-flaw / falsifier selection) and whether stated confidence is calibrated, with judge-free MCQ axes plus open-ended critique scoring.https://bgpt.pro/refutebgpt-refutebiotools:bgpt-refuteWeb applicationPythonMITFree of chargeOpen accesshttps://github.com/connerlambden/refute-inspectRepositoryhttps://huggingface.co/datasets/BGPT-OFFICIAL/refuteOtherHugging Face datasethttps://doi.org/10.5281/zenodo.21542238OtherZenodo preprint DOIhttps://www.openml.org/d/47266OtherOpenML REFUTE-knowledge-v3https://www.openml.org/d/47268OtherOpenML REFUTE-soundness-v3https://doi.org/10.7910/DVN/IGAJWOOtherHarvard Dataverse datasethttps://ascl.net/code/v/4795OtherASCL software entryhttps://www.wikidata.org/wiki/Q140690703OtherWikidata itemhttps://osf.io/qxyfe/OtherOSF projecthttps://www.saashub.com/refuteOtherSaaSHub listinghttps://bgpt.pro/refuteGeneral10.5281/zenodo.21542238PrimaryInterim preprint deposit on Zenodo (v3.0.0-preprint).Conner Lambdencontact@bgpt.prohttps://bgpt.prohttps://orcid.org/0000-0003-0162-6622PersonDeveloperBGPT REFUTEOpen benchmark for scientific critique honesty and epistemic calibration on recent biomedical literature.https://bgpt.pro/refutebgpt_refutebiotools:bgpt_refuteREFUTEREFUTE is an open benchmark for scientific critique honesty and epistemic calibration on recent life-science and biomedical literature. It tests whether models keep claims inside what the evidence allows (overclaim / planted-flaw / falsifier selection) and whether stated confidence is calibrated, with judge-free MCQ axes plus open-ended critique scoring.https://bgpt.pro/refuterefutebiotools:refutePomelo2Statistical analysis of differential expression, including linear models and permutation testshttp://pomelo2.iib.uam.es/pomelo2biotools:pomelo2http://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3316Computer sciencehttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_0091BioinformaticsLinuxMacWindowsRJavaScriptPythonhttp://pomelo2.iib.uam.es/RepositoryGithub repository for source code access and downloadhttp://pomelo2.iib.uam.es/help/pomelo2-help.htmlGeneralPomelo2 main documentation resourcemgnifamBuild protein families from sequence clusters by iterative HMM search over very large databases — streaming, deterministic, pyHMMER-based.https://github.com/vagkaratzas/mgnifammgnifambiotools:mgnifam1.0.0PrimerDesignerA practical guide for designing primers for SNVs/indels, allele-specific PCR, and structural variants, plus SilicoPCR for checking existing primer pairs — including input formats, result interpretation, and reporting.https://genometaster.charite.de/primer-designerprimerdesignerbiotools:primerdesignerWeb applicationhttp://edamontology.org/topic_3168SequencingEmergingFree of chargehttps://genometaster.charite.de/primer-designerRepositoryThe repository is publicly available on Github.CBRAWorkflow optimized for the analysis of rare diseases, designed to detect SNVs, INDELs , CNVs and SVs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow and following nf-core standards. It has an advanced variant annotation optimized for rare diseases diagnosis and discovery.https://github.com/CIBERER/CBRAnf-cbra-snvsbiotools:nf-cbra-snvsWorkflowhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0091BioinformaticsLinuxMITIMPaCT-ISCIIIIMPaCT-DataEmergingFree of chargeOpen accesshttps://github.com/CIBERER/CBRARepositoryhttps://github.com/CIBERER/CBRAUser manualgcscreenOpen-source R package for the analysis of kinetic phenotypic screens read as growth curves in 96-well microplates. Implements a benchmarked, simulation-validated pipeline that goes from raw OD600 trajectories to a hit list: plate-level quality control (control CV, Z'-factor, SSMD), within-plate positional correction by median polish (B-score), normalisation to the median of in-plate controls, and hit calling requiring convergence between per-plate ANOVA and a library-wide linear mixed model with Benjamini-Hochberg FDR control. Also extracts kinetic parameters (maximum specific growth rate, maximum OD, lag time) and supports functional principal component analysis and Monte Carlo validation of pipeline operating characteristics.https://github.com/mparmol/gcscreengcscreenbiotools:gcscreen0.1.0ICTV to NCBITaxon SSSOM mappingThe ICTV to NCBITaxon SSSOM mapping is a curated cross‑reference dataset that links official ICTV virus taxa to their corresponding NCBI Taxonomy identifiers using the SSSOM (Simple Standard for Sharing Ontology Mappings) format. It provides machine‑readable, standardized mappings that enable interoperability between the ICTV taxonomy and widely used NCBI Taxonomy resources.https://github.com/EVORA-project/virus-taxonomy-mappingsictv_to_ncbitaxon_sssom_mappingbiotools:ictv_to_ncbitaxon_sssom_mappingICTV Ontology APIICTV Ontology API
The ICTV Ontology API is a structured, machine‑readable interface that exposes the complete ICTV virus taxonomy as an OWL ontology. It provides programmatic access to official virus taxa, their hierarchical relationships, synonyms, historical names, and metadata, enabling automated reasoning, name resolution, and integration of ICTV taxonomy into bioinformatics tools and databases. Key capabilities include access to the full taxonomy (realms to species), querying taxon relationships, retrieving release and status metadata, supporting OWL/RDF reasoning workflows, and integration with tools such as the ICTV Taxon Resolver (bio.tools/ictv_taxon_resolver), which relies on the API for taxon name resolution. Citation: Lieutaud et al., 2026, bioRxiv, https://doi.org/10.64898/2026.06.16.732600.https://evora-project.github.io/ictv-ontology/helpers/ictv_ontology_apibiotools:ictv_ontology_apiICTV Taxon resolverThe ICTV Taxon Resolver is an online lookup tool that uses the ICTV Ontology API to translate any virus name—current, historical, informal, or deprecated—into its official, up‑to‑date taxonomic position within the ICTV (International Committee on Taxonomy of Viruses) taxonomy, the globally recognized standard for virus classification.https://ictvapi.evora-project.eu/ictv_taxon_resolverbiotools:ictv_taxon_resolverLIGPLOTProgram which plots schematic diagrams of protein-ligand interactions.http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ligplotbiotools:ligplotDesktop applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMachttp://edamontology.org/operation_0482Protein-ligand dockinghttp://www.mybiosoftware.com/ligplot-4-5-3-ligplot-1-3-plot-schematic-diagrams-protein-ligand-interactions.htmlSoftware cataloguehttp://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/manual/User manualhttp://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/faq.htmlGeneral10.1093/protein/8.2.127763088210.1021/ci200227u21919503Roman Laskowskiroman@ebi.ac.ukhttp://www.ebi.ac.uk/~roman/PersonPrimary contactClustVisWeb tool which allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as a file or by copy-pasteing it to the text box.http://biit.cs.ut.ee/clustvisclustvisbiotools:clustvis1RRID:SCR_017133rridWeb applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowsMacRGPL-3.0Elixir-EEFree of chargeToolsEstoniahttp://edamontology.org/operation_0313Gene expression clusteringhttp://edamontology.org/operation_2942Treemap visualisationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2939Principal component plottinghttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/data_3111Processed microarray datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_3113Sample annotationhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_0928Gene expression profilehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttps://github.com/taunometsalu/ClustVisRepositoryA code repository in github.https://hub.docker.com/r/taunometsalu/clustvis/Container fileDocker imagehttps://biit.cs.ut.ee/clustvis/General10.1093/nar/gkv46825969447PMC4489295PrimaryELIXIR-EEInstituteProviderTauno Metsalutauno.metsalu@ut.eePersonPrimary contactbiit.support@ut.eePersonPrimary contactGlycoDashGlycoDash is an R Shiny dashboard for processing glycomics data obtained from LaCyTools, SweetSuite and Skyline.https://github.com/Center-for-Proteomics-and-Metabolomics/GlycoDashGlycoDashbiotools:GlycoDashv1.11.5-masterhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_0121ProteomicsRMITEmerginghttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3620xlsxhttps://github.com/Center-for-Proteomics-and-Metabolomics/GlycoDash/releases/download/v1.11.5-master/GlycoDash_user_guide_v1.11.5.pdfUser manualskylineuses10.1007/s00216-025-05794-339985669PMC11961463Rosin-Rammler Diagram plotting toolThis tool plots the Rosin-Rammler Diagram (RRSB) and calculates various related parameters.https://www.mathworks.com/matlabcentral/fileexchange/28013-rosin-rammler-diagram-plotting-toolrrsb-plotbiotools:rrsb-plot1.16.0.0Libraryhttp://edamontology.org/topic_3344Biomedical sciencehttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3382ImagingWindowsLinuxMacMATLABMATLABFile ExchangeFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0337Visualisationhttps://www.mathworks.com//matlabcentral/mlc-downloads/downloads/submissions/28013/versions/17/screenshot.pngScreenshotIvan Brezanihttps://www.mathworks.com/matlabcentral/profile/2241235-ivan-brezaniPersonPrimary contactMOODSA suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. MOODS can also process high-order PWMs with dependencies between adjacent positions and sequence variants such as SNPs, insertions and deletions.https://www.cs.helsinki.fi/group/pssmfind/moodsbiotools:moodsCommand-line toolScripthttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0157Sequence composition, complexity and repeatsLinuxC++PythonGPL-3.0Animal and Crop Genomicshttp://edamontology.org/operation_0239Sequence motif recognitionhttps://github.com/jhkorhonen/MOODSRepositoryhttps://github.com/jhkorhonen/MOODS/issuesIssue trackerhttps://github.com/jhkorhonen/MOODS/wiki/Getting-startedGeneral10.1109/tcbb.2009.3521071798Primary10.1093/bioinformatics/btw68328011774Primary10.1093/bioinformatics/btp55419773334PMC2778336Primaryjanne.h.korhonen@aalto.fiPersonPrimary contactSupernovaSupernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances. Almost all other methods instead merge homologous chromosomes into single incorrect 'consensus' sequences. Supernova is the only practical method for creating diploid assemblies of large genomes.https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcomesupernovabiotools:supernovaSuiteWorkflowCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0196Sequence assemblyLinuxProprietaryhttp://edamontology.org/operation_3933Demultiplexinghttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_3192Sequence trimminghttps://support.10xgenomics.com/de-novo-assembly/software/downloads/latestDownloads pagehttps://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/installationInstallation instructionshttps://support.10xgenomics.com/de-novo-assembly/software/release-notes/2-1Release notes10.1101/gr.214874.11628381613PMC5411770PrimaryDavid B. Jaffedavid.jaffe@10xgenomics.comPersonPrimary contact10x Genomicssupport@10xgenomics.comhttps://10xgenomics.comInstitutePangolinPangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences.https://github.com/tkzeng/Pangolinpangolinbiotools:pangolinCommand-line toolhttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3676Exome sequencingMacLinuxWindowsPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3752CSV10.1186/s13059-022-02664-435449021PMC9022248Yang I Liyangili1@uchicago.eduhttps://orcid.org/0000-0002-0736-251XPersonTony ZengITSoneWBITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing.http://itsonewb.cloud.ba.infn.it/galaxyitsonewbbiotools:itsonewbhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3168SequencingASAPASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments.
ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.https://bioinfo.mnhn.fr/abi/public/asapasap-assemblebiotools:asap-assembleWeb applicationDesktop applicationhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/operation_3478Phylogenetic reconstructionhttp://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_3359Splittinghttps://bioinfo.mnhn.fr/abi/public/asap/help_asap.htmlGeneralhttps://bioinfo.mnhn.fr/abi/public/asap/FAQ_asap.htmlFAQ10.1111/1755-0998.1328133058550Nicolas Puillandrepuillandre@mnhn.frPersonJGI Genome PortalThe JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms.http://genome.jgi.doe.gov/jgi_genome_portalbiotools:jgi_genome_portalRRID:SCR_002383rridDatabase portalhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacJavahttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/operation_0362Genome annotationhttps://jgi.doe.gov/user-program-info/General10.1093/nar/gkr94722110030PMC3245080I.V. Grigorievivgrigoriev@lbl.govPersonPrimary contactChimeraXStructure visualization for researchers, educators, and developers.
Tutorials can be viewed in any browser, but those with click-to-execute links should be viewed from within ChimeraX for the links to work. To view a web page from within ChimeraX, start ChimeraX and use the command open URL (substituting in the actual URL), or navigate here using the ChimeraX menu: Help... Tutorials.
UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.https://www.rbvi.ucsf.edu/chimeraxchimeraxbiotools:chimeraxhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0605Informaticshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3794RNA immunoprecipitationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0387Molecular surface calculationhttp://edamontology.org/operation_0480Side chain modellinghttp://edamontology.org/operation_0478Molecular dockinghttps://www.rbvi.ucsf.edu/chimerax/gallery.htmlOtherhttps://www.rbvi.ucsf.edu/chimerax/features.htmlGeneralhttps://www.rbvi.ucsf.edu/chimerax/tutorials.htmlTraining materialartiaxincludes10.1002/pro.394332881101PMC773778810.1002/pro.323528710774PMC5734306Thomas E. Ferrintef@cgl.ucsf.eduhttps://orcid.org/0000-0001-6227-0637PersonCyTargetLinkerA flexible solution for network extension in Cytoscape | The CyTargetLinker app extends biological networks with regulatory interactions, for example miRNA-target, TF-target or drug-target interactions | CyTargetLinker website and tutorials | CyTargetLinker - Extend your biological networks in Cytoscapehttps://cytargetlinker.github.io/CyTargetLinkerbiotools:CyTargetLinkerhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0204Gene regulationJavahttp://edamontology.org/operation_3439Pathway or network predictionhttp://edamontology.org/operation_0277Pathway or network comparisonhttp://edamontology.org/operation_1781Gene regulatory network analysishttp://apps.cytoscape.org/apps/cytargetlinkerRepositoryhttps://github.com/CyTargetLinker/cytargetlinker/issuesIssue trackerhttps://cytargetlinker.github.io/pages/citationCitation instructionshttps://cytargetlinker.github.io/pages/docsGeneral10.12688/F1000RESEARCH.14613.231489175PMC670739610.1371/journal.pone.008216024340000PMC3855388Martina Kutmonmartina.kutmon@maastrichtuniversity.nlhttps://orcid.org/0000-0002-7699-8191PersonDRAMDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomeshttps://github.com/WrightonLabCSU/DRAMdrambiotools:dramhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3071Biological databaseshttp://edamontology.org/topic_3321Molecular geneticshttp://edamontology.org/operation_3672Gene functional annotationhttps://github.com/WrightonLabCSU/DRAMRepositoryhttps://github.com/WrightonLabCSU/DRAM/wikiGeneral10.1093/nar/gkaa621ArrayAnalysisArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.https://www.arrayanalysis.orgarrayanalysis.orgbiotools:arrayanalysis.orgWeb applicationhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_0091BioinformaticsLinuxWindowsMacRCC-BY-4.0Free of chargeOpen accesshttps://www.arrayanalysis.orgGeneral10.1093/nar/gkt29323620278PMC369204910.1186/s12864-015-1689-826122086PMC448612610.64898/2026.07.13.738193PreprintJarno Koetsierhttps://orcid.org/0000-0002-7981-1345PersonDeveloperMaintainerLars Eijssenhttps://orcid.org/0000-0002-6473-2839PersonDeveloperPinPathPinPath enables flexible visualization of (omics) data onto pathways diagrams, allowing users to pinpoint where the relevant changes occur. It supports pathway diagrams from WikiPathways and KEGG, as well as custom GPML and KGML files. Data can be displayed on both native pathway layouts and network representationshttps://synum-lab.github.io/PinPath-web/pinpathbiotools:pinpathWeb applicationLibraryCommand-line toolhttp://edamontology.org/topic_3391Omicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksRMITBioconductorFree of chargeOpen accesshttps://github.com/SyNUM-lab/PinPathRepositoryhttps://synum-lab.github.io/PinPath-web/Generalhttps://doi.org/doi:10.18129/B9.bioc.PinPathUser manualJarno Koetsierjarno.koetsier@maastrichtuniversity.nlhttps://orcid.org/0000-0002-7981-1345PersonPrimary contactDeveloperMaintainerLars Eijssenhttps://orcid.org/0000-0002-6473-2839PersonContributorEgon Willighagenhttps://orcid.org/0000-0001-7542-0286PersonContributorrun_dbcanStandalone version of dbcan to run CAZyme and CGC annotation.https://github.com/bcb-unl/run_dbcan/run_dbcanbiotools:run_dbcanv5.2.9dbcan3Updated web server version of dbCAN2 for CAZyme/CGC annotation and substrate predictionhttps://pro.unl.edu/dbCAN2/dbcan3biotools:dbcan3v310.1093/nar/gkad32837125649PMC10320055pickletBrowser-based tool to open almost any sequence file — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR and more — see every sequence inside, pick the ones you want, and save them as FASTA. The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open. Runs entirely in the browser — files are never uploaded.https://fishka.bio/pickletpickletbiotools:pickletDesktop applicationWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementWindowsMacLinuxTypeScriptFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_2121Sequence file editinghttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1632SCFhttp://edamontology.org/format_3000AB1http://edamontology.org/format_1963UniProtKB formathttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1912Nexus formathttps://fishka.bioSoftware cataloguefishka.bio — the tool collection picklet belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no server10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including picklet.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerab1lensBrowser-based viewer for Sanger sequencing chromatograms in AB1/ABIF and SCF format. Opens .ab1/.abi/.fsa files, shows raw and analysed traces, basecalls, quality values and the ABIF directory, and puts two reads side by side for comparison. Aligns a read against a reference sequence to highlight mismatches. Exports the read as FASTA, FASTQ or ABIF and the chromatogram as a high-resolution image. Runs entirely in the browser — files are never uploaded.https://fishka.bio/ab1lensab1lensbiotools:ab1lensWeb applicationDesktop applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationWindowsMacLinuxTypeScriptFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_1632SCFhttp://edamontology.org/format_3000AB1http://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1929FASTAhttps://fishka.bioSoftware cataloguefishka.bio — the tool collection ab1lens belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no server10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including ab1lens.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainergbatlasBrowser-based viewer for GenBank and GenPept files. Renders an interactive linear and circular feature map, the annotated source text, and the nucleotide/protein sequence side by side.
Translates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Handles multi-record files. Runs entirely in the browser — files are never uploaded.https://fishka.bio/gbatlasgbatlasbiotools:gbatlasWeb applicationDesktop applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsWindowsMacLinuxTypeScriptFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/operation_0436Coding region predictionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1937genpepthttps://fishka.bioSoftware cataloguefishka.bio — the tool collection gbatlas belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no server10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including gbatlas.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerMol Biology ToolsMolecular Biology Tools is a free browser-based collection of molecular biology utilities for routine sequence analysis, primer design, Sanger sequencing primer planning, cloning setup, and wet-lab calculations. The site includes tools for PCR primer design, Sanger primer design and primer walking, primer binding checks, restriction site analysis, reverse complement generation, ORF and protein translation, codon optimization, ligation calculations, molarity calculations, dilution calculations, and multi-solute solution recipe preparation. The tools run in the browser and are intended for quick experimental planning, without requiring logins or uploading sequences to the server.https://molbiologytools.com/mol_biology_toolsbiotools:mol_biology_toolsWeb servicehttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_3895Synthetic biologyhttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3125DNA binding sitesAndroidMacWindowsiOSLinuxJavaScriptProprietaryEmergingFree of chargehttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/operation_0489Genetic code predictionhttp://edamontology.org/operation_0363Reverse complementhttp://edamontology.org/operation_0436Coding region predictionhttp://edamontology.org/operation_2419Primer and probe designhttp://edamontology.org/operation_0398Protein molecular weight calculationhttps://molbiologytools.com/Software catalogueRepositoryLanding page with all tools listed.https://molbiologytools.com/faqOtherSearchable FAQ covering primer design, Sanger sequencing, restriction sites, sequence checks, molarity, dilution, ligation, and connected tool workflows.https://molbiologytools.com/primer_designServicePCR primer design tool for raw DNA, FASTA, or GenBank templates, with primer length or target Tm modes and optional restriction-enzyme overhang planning.https://molbiologytools.com/primer_binding_checkerServicePrimer binding checker for linear or circular DNA templates, including binding positions, amplicon size, strand direction, and product checks.https://molbiologytools.com/restriction_site_analyzerServiceRestriction enzyme site analyzer for linear or circular DNA, FASTA, or GenBank input, with enzyme cut-site detection and sequence-to-primer workflow links.https://molbiologytools.com/molarity_calculatorServiceThis free online molarity calculator handles single-solute mass, molarity, final-volume and g/L calculations, liquid acid stocks, and protein molarity conversions using molecular weight in kDahttps://molbiologytools.com/ligation_calculatorServiceDNA ligation calculator for cloning setup, vector mass, insert length, insert-to-vector molar ratio, and insert mass calculation.https://molbiologytools.com/sanger_primer_designerServiceFree online Sanger sequencing primer design tool for primer walking, target coverage, high-quality read planning, and binding validation.https://molbiologytools.com/orf_protein_translatorServiceFree online ORF finder and DNA to protein translator for open reading frames, coding-region checks, amino acid translation, and expression planning.https://molbiologytools.com/codon_optimizerServiceCodon Optimizer is a free online optimization tool for preserving the translated protein sequence while checking GC content, codon changes, and downstream primer design.https://molbiologytools.com/dilution_calculatorServiceFree online dilution calculator for C1V1 logic, prepared stock solutions, and antibody 1:N ratios; molecular weight is required only for cross-unit conversion.https://molbiologytools.com/buffer_calculatorServiceA free online tool for preparing common lab buffer recipes by target pH, buffer strength, salt form, and final volume.https://molbiologytools.com/reverse_complementServiceGenerate a reverse complement, complement, reversed sequence, or cleaned DNA from plain-text, FASTA, or GenBank input, with full IUPAC ambiguity-code supporthttps://molbiologytools.com/help_guidesQuick start guideDr. Rohit P Jamesrpjscience@gmail.comhttps://orcid.org/0009-0003-9347-2014PersonPrimary contactDeveloperMaintainerProviderDr. Rohit P James graduated from IIT Bombay. He works on biocatalysis and enzyme engineering.Trace4HarmonizationHarmonize numerical values extracted from medical images (e.g. acquired with different models of image-acquisition system)http://deeptracetech.com/trace4harmonizationbiotools:trace4harmonizationv1.0.00Command-line toolLibraryDesktop applicationhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_2269Statistics and probabilityWindowsLinuxMATLABPythonProprietaryEUCAIMEmergingCommercialRestricted accesshttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/trace4harmonization/artifacts-tabRepositoryHarbor LinkRectangleDocumentation
Rectangle is an open-source Python package for single-cell-informed cell-type deconvolution of bulk and spatial transcriptomic data.
Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical signature building for fine-grained cell-type deconvolution, estimation and correction of unknown cellular content, and efficient handling of large-scale single-cell data during signature matrix computation.
Rectangle was developed to overcome the current challenges in cell-type deconvolution, providing a robust and accurate methodology while ensuring a low computational profile.https://github.com/ComputationalBiomedicineGroup/Rectanglerectanglebiotools:rectanglehttps://rectanglepy.readthedocs.io/API documentation10.64898/2026.07.07.736950PreprintkMetaShotThe application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting.https://github.com/gdefazio/kMetaShotkMetaShotbiotools:kMetaShotCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0EmergingFree of chargeOpen accessToolsMarine MetagenomicsItalyhttps://github.com/gdefazio/kMetaShotOther10.1093/bib/bbae680Giuseppe Defaziogiuseppe.defazio@uniba.ithttps://persone.ict.uniba.it/rubrica/@@cerca?advanced_search=False&sort_on=&SearchableText=defaziohttps://orcid.org/0000-0002-9356-5224PersonDeveloperPost-Doc Researcher at University of BariTranscriptoScopeLocal Windows-friendly R Shiny application for RNA-seq differential expression using DESeq2, normalized-expression testing, over-representation analysis, fgsea-ranked pathway analysis, and WGCNA coexpression-network analysis. It supports input validation, additive and interaction designs, built-in human, fruit-fly, and yeast annotations, publication-quality plots, and reproducibility bundles containing results, settings, and executable R and R Markdown rerun code.https://github.com/Shettima123/TranscriptoScopetranscriptoscopebiotools:transcriptoscope0.5.0WorkbenchDesktop applicationhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-SeqWindowsRMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/operation_3928Pathway analysishttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_3766Weighted correlation network analysishttp://edamontology.org/operation_3223Differential gene expression profilinghttps://github.com/Shettima123/TranscriptoScopeRepositoryhttps://github.com/Shettima123/TranscriptoScope/issuesIssue trackerhttps://github.com/Shettima123/TranscriptoScope/releases/download/v0.5.0/TranscriptoScope_Windows_Store_v0.5.0.exeBinariesStandalone x64 Windows installer that bundles R and the required package library.0.5.0https://github.com/Shettima123/TranscriptoScope/releases/download/v0.5.0/TranscriptoScope_Windows_v0.5.0.zipSoftware packageManual Windows package for users who already have R.0.5.0https://github.com/Shettima123/TranscriptoScope/archive/refs/tags/v0.5.0.zipSource code0.5.0https://github.com/Shettima123/TranscriptoScope/releases/tag/v0.5.0Downloads page0.5.0https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/README.mdGeneralhttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/INSTALL_WINDOWS.mdInstallation instructionsQuick start guidehttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/RELEASE_NOTES.mdRelease noteshttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/CITATION.cffCitation instructionshttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/SUPPORT.mdGeneralSupport and issue-reporting instructions.10.5281/zenodo.21409091Primary0.5.0Version-specific archived software release.Abubakar Abdulkadirhttps://github.com/Shettima123PersonDeveloperMaintainerDocumentorPrimary contactDr. Rosby's LabProjectProviderSupportSouthern University A and MInstituteProviderkegg-pathways-completeness-toolThis tool estimates the completeness of KEGG pathway modules from the presence or absence of KEGG orthologues (KOs)https://github.com/EBI-Metagenomics/kegg-pathways-completeness-toolkegg-pathways-completeness-toolbiotools:kegg-pathways-completeness-tool1.4.3Command-line toolhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksShellPythonApache-2.0Maturehttp://edamontology.org/operation_0533Expression profile pathway mappinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_3475TSVhttps://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool#theory--backgroundOtherhttps://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool/blob/master/docs/parse_hmmer_table.mdUser manualHow to Generate KO-Annotated Tablehttps://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool/blob/master/docs/update_database.mdUser manualUpdate KEGG Modules Database10.1093/nar/gkac108036477304PMC9825492Primarymtagmtag is a Python-based command line tool for jointly analyzing multiple sets of GWAS summary statistics as described by Turley et. al. (2018). It can also be used as a tool to meta-analyze GWAS results.https://github.com/JonJala/mtagmtagbiotools:mtag0.9.0Command-line toolhttp://edamontology.org/topic_3517GWAS studyPerlPythonRGPL-3.0Maturehttp://edamontology.org/operation_3209Genome comparisonhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttps://github.com/JonJala/mtag/wikiGeneral10.1038/s41588-017-0009-429292387PMC5805593PrimarysubTOMSubvolume processing scripts with the TOM toolbox is a collection of scripts form a pipeline for subvolume alignment and averaging of electron cryo-tomography data.https://github.com/DustinMorado/subTOMsubTOMbiotools:subTOMScripthttp://edamontology.org/topic_0611Electron microscopyLinuxShellCMATLABMITMaturehttp://edamontology.org/operation_3552Microscope image visualisationhttps://subtom.readthedocs.io/en/latest/index.htmlGeneralminimodA bioinformatics tool for viewing and calculating base modification frequencies from BAM fileshttps://warp9seq.github.io/minimodminimodbiotools:minimodv0.5.0Command-line toolhttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_3674Methylated DNA immunoprecipitationLinuxC++ShellPythonCMITMaturehttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1929FASTAhttps://warp9seq.github.io/minimodGeneral10.1101/2025.07.16.665072Preprintmetilene3metilene³ is a computational tool for identifying Differentially Methylated Regions (DMRs) across multiple conditions, supporting both supervised and unsupervised analyses, and enables the construction of Differentially Methylated Trees for epigenetic relationship inference and sample clustering.https://github.com/zzhu1372/metilene3metilene3biotools:metilene3v3.1Command-line toolhttp://edamontology.org/topic_3295EpigeneticsMacLinuxCPythonGPL-2.0Maturehttp://edamontology.org/operation_3809DMR identificationhttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_3432Clusteringhttps://zzhu1372.github.io/metilene3-doc/Generalhttps://zzhu1372.github.io/metilene3-doc/docs/guide/quick.htmlQuick start guide10.1038/s41467-026-74931-y42401582Primarynf-testSimple test framework for Nextflow pipelineshttps://www.nf-test.com/nf-testbiotools:nf-testv0.9.5Command-line toolShellJavaGroovyMITMaturehttps://www.nf-test.com/Otherhttps://www.nf-test.com/docs/getting-started/Quick start guide10.1093/gigascience/giaf13041124057PMC12616847PrimaryCebraEMCebraEM is a bioinformatics tool for analyzing and processing large-scale imaging data, providing a pipeline for segmentation, annotation, and analysis with support for both Linux and Windows environments. It includes modules for core functionality, annotation, and network analysis, requiring specific dependencies and a conda environment for execution.https://github.com/jhennies/CebraEMCebraEMbiotools:CebraEMv0.0.3bCommand-line toolhttp://edamontology.org/topic_0611Electron microscopyLinuxWindowsShellPythonMITMaturehttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_3553Image annotationhttps://github.com/jhennies/CebraEM/blob/main/cebra-em/README.mdGeneral10.1101/2023.04.06.535829Preprintblue-crabblue-crab is a tool to convert from ONT POD5 format to the community maintained SLOW5/BLOW5 format. Lossless nanopore pod5 s/blow5 file conversion.https://github.com/Psy-Fer/blue-crabblue-crabbiotools:blue-crabv0.5.0Command-line toolhttp://edamontology.org/topic_0622GenomicsShellPythonMITMaturehttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2977Nucleic acid sequencehttps://github.com/Psy-Fer/blue-crab/blob/main/docs/cli.mdCommand-line optionshttps://github.com/Psy-Fer/blue-crab/blob/main/README.mdGeneral10.1038/s41587-021-01147-434980914PMC9287168Primary10.1093/gigascience/giaf11841100284PMC12530089PrimaryFAIR EVA for EUCAIMFAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.
This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.https://github.com/IFCA-Advanced-Computing/FAIR_evafair_eva_4_eucaimbiotools:fair_eva_4_eucaimEUCAIM_plugin_0.3EUCAIM_plugin_0.3.1EUCAIM_plugin_0.4.0EUCAIM_0.4.2v0.6.1Command-line toolPlug-inWeb servicehttp://edamontology.org/topic_4012FAIR dataLinuxPythonApache-2.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_0336Format validationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_1048Database IDfair-eva-cli batch -p eucaim_legacyhttps://github.com/IFCA-Advanced-Computing/FAIR_evaRepositoryRepository for FAIR EVA, without the EUCAIM specific pluginhttps://gitlab.ifca.es/eucaim/fair_eucaimRepositoryRepository for FAIR-EVA for eucaim plugin. Currently not public.https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.mdGeneralDocumentation for the main package, EUCAIM plugin specific documentation not included.https://gitlabpages.ifca.es/fair-eva-guide-608baa/User manualWiki page with FAIR EVA for EUCAIM specific instructions.10.1038/s41597-023-02652-8Fernando Aguilarhttps://orcid.org/0000-0001-9462-4831PersonDeveloperMaintainerDocumentorCreator and devloper of the main package FAIR EVA.
This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.David Rodríguezhttps://orcid.org/0000-0002-9160-5106PersonDeveloperPrimary contactDeveloper of the EUCAIM plugin.Inés Victoriahttps://orcid.org/0009-0003-7950-3937PersonDeveloperDeveloper of the EUCAIM plugin.trackastraTrackastra is a transformer-based cell-tracking tool for live-cell microscopy. It links already segmented cell instances across time by predicting associations between detections. It supports greedy tracking with or without cell divisions, optional ILP-based linking, pretrained tracking models, and export of tracked masks and lineage information in Cell Tracking Challenge format.https://github.com/bioinfbrad/trackastra-galaxytrackastra-galaxybiotools:trackastra-galaxy0.5.3Command-line toolhttp://edamontology.org/topic_3385Light microscopyLinuxPythonBSD-3-ClauseEmergingFree of chargeToolsTrainingComputehttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFLink already segmented cell instances across a microscopy time series and produce tracked masks, lineage information and association edges.trackastra track --imgs images/ --masks masks/ --output-ctc tracked_ctc --output-edge-table edges.csv --model-pretrained general_2d --mode greedyhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFLink already segmented cell instances across a microscopy time series and produce tracked masks, lineage information and association edges.trackastra track --imgs images/ --masks masks/ --output-ctc tracked_ctc --output-edge-table edges.csv --model-pretrained general_2d --mode greedyhttps://github.com/weigertlab/trackastraRepositoryhttps://pypi.org/project/trackastra/Downloads pagepypi installation5.3https://anaconda.org/channels/conda-forge/packages/trackastra/overviewDownloads pageConda installation5.3https://github.com/weigertlab/trackastraCommand-line optionsGitHub repository10.1007/978-3-031-73116-7_27OtherPeer-reviewed publication describing the Trackastra transformer-based method for tracking segmented cells in live-cell microscopy.InflexaInflexa is an open-source, agentic orchestration platform for computational biology and translational medicine. It is designed to assist researchers in analyzing multi-omics, cheminformatics, and imaging data by reading published literature, designing multi-step analysis plans, and executing experiments with full reproducibility.https://inflexa.aiinflexabiotools:inflexaCommand-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_3391OmicsLinuxMacWindowsPythonTypeScriptGoApache-2.0Free of chargeOpen accesshttp://edamontology.org/operation_2945Data analysishttps://github.com/inflexa-ai/inflexaRepositoryGitHub repohttps://public.inflexa.ai/GSE110256/pharmacogenomic-mouse-cerebrocortical-culturesOtherPharmacogenomic Drug Screen in Mouse Cerebrocortical Cultures (Re-analysis of GSE110256)https://public.inflexa.ai/GSE282861/il-33-il-4ra-blockade-hdm-airway-inflammationOtherGenome-wide Dissection of IL-33 and IL-4Rα Blockade in HDM-driven Airway Inflammation (Re-analysis of GSE282861)https://public.inflexa.ai/33558495/breast-cancer-african-arab-european-ancestryOtherHow Genetic Ancestry Shapes Breast Cancer Biology (Re-analysis of Roelands et al. 2021 (npj Breast Cancer) )https://public.inflexa.ai/GSE286094-GSE286095/atg7-deficiency-reshapes-microglia-biology-alzheimers-diseaseOtherATG7 Deficiency Reshapes Microglia Biology in Alzheimer’s Disease (Re-analysis of GSE286094 / GSE286095)https://public.inflexa.ai/GSE157194/atopic-dermatitis-dupilumab-cyclosporineOtherAtopic Dermatitis Transcriptome Under Dupilumab and Cyclosporine (Re-analysis of GSE157194)https://github.com/inflexa-ai/inflexa/releasesBinariesSupportsupport@inflexa.aiSupportREACTRReactr is an modularized, Snakemake workflow for automated, species-agnostic characterization of gene families from sequence to experimental design. Given a query protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions), reactr retrieves genomic data and runs comprehensive analysis across 4 integrated tiers: (1) evolutionary analysis, including homolog detection, domain-based clustering, multiple sequence alignment, and phylogenetic inference; (2) synteny and selection analysis, detecting collinear blocks and calculating Ka/Ks ratios; (3) structural and regulatory characterization, including motif discovery, chromosomal mapping, biochemical property prediction, subcellular localization prediction, and promoter analysis; and (4) experimental design tools, generating PCR primers and scored CRISPR gRNAs for lab validation. Reactr bridges computational prediction and experimental validation, thus enabling rapid transition from genomic discovery to functional studies.https://zenodo.org/records/21125109reactrbiotools:reactr3Command-line toolhttp://edamontology.org/topic_0091BioinformaticsMacPythonMITBiocondaFree of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalLoads genomic data and prepares it for query analysis`snakemake -s LoadDatasets.smk --cores 8`http://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_2928Alignmenthttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_2990ClassificationRuns query analysis`snakemake -s MainPipeline.smk`