SNP-sitesFinds SNP sites from a multi-FASTA alignment file.https://sanger-pathogens.github.io/snp-sites/snp-sitesbiotools:snp-sites2.5.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_2885DNA polymorphismLinuxCGPL-3.0Open accesshttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCF

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCF

snp-sites my_alignment.aln snp-sites my_gzipped_alignment.aln.gzhttps://github.com/sanger-pathogens/snp-sitesRepositoryhttps://sanger-pathogens.github.io/snp-sites/General10.1099/mgen.0.00005628348851PMC5320690PrimaryParseSNPA small <720Kb C++ windows utility. That allows you to load Ancestry, 23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert them to Ancestry format. But also create files from peer reviewed publications to compare with you loaded data to give your genetic disposition for the condition you have entered the data for an statistical risk if OR values are included. Included with the program are example files for Type 2 Diabetes risk factors. (As I have type 2 Diabetes so I could test the results).https://britrobin.github.io/ParseSNP/parsesnp21-26biotools:parsesnp21-261.1.1Desktop applicationhttp://edamontology.org/topic_3577Personalised medicineWindowsC++GPL-3.0EmergingFree of chargeOpen accesshttps://britrobin.github.io/ParseSNP/OtherGit page for easy installer and pdf manual downloadhttps://github.com/BritRobin/ParseSNPRepositoryGitHub repositoryhttps://britrobin.github.io/ParseSNP/Software packageWindows x64 or x86 installer1.1.1https://raw.githubusercontent.com/BritRobin/ParseSNP/master/ParseSNP_Manual.pdfUser manualpdf user manualCompuCell3DCompuCell3D is a multiscale multicellular virtual tissue modeling and simulation environment. CompuCell3D is written in C++ and provides Python bindings for model and simulation development in Python.https://compucell3d.org/SrcBincompucell3dbiotools:compucell3d4.8.0Command-line toolhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3307Computational biologyWindowsLinuxMacPythonC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_2426Modelling and simulationhttps://compucell3d.org/SrcBinRepositoryhttps://www.reddit.com/r/CompuCell3D/Discussion forumhttps://compucell3d.org/API documentationhttps://compucell3d.org/TutorialsTraining materialhttps://compucell3d.org/PublicationsCitation instructions10.1016/b978-0-12-388403-9.00013-822482955PMC3612985PrimaryNuclearPhaserNuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.https://github.com/JanaSperschneider/NuclearPhasernuclearphaserbiotools:nuclearphaser1.1Scripthttp://edamontology.org/topic_0622GenomicsLinuxMacPythonGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttps://github.com/JanaSperschneider/NuclearPhaserRepositoryhttps://github.com/JanaSperschneider/NuclearPhaser/blob/main/README.mdQuick start guideJana Sperschneiderhttps://github.com/JanaSperschneiderGenErodeWorkflow for whole genome sequencing analysis, including patterns of genome erosion. Written in Snakemake workflow language.https://github.com/NBISweden/GenErodegenerodebiotools:generodeWorkflowhttp://edamontology.org/topic_0622GenomicsOtherGPL-3.0Maturehttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_3003BED

http://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAM

http://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAM

http://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCF

https://github.com/NBISweden/GenErodeGeneralhttps://github.com/NBISweden/GenErode/wikiUser manual10.1186/s12859-022-04757-035698034PMC9195343MethodbiokangaBioKanga is an integrated toolkit of high performance bioinformatics subprocesses targeting the challenges of next generation sequencing analytics. Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.https://github.com/csiro-crop-informatics/biokangabiokangabiotools:biokanga4.4.2Suitehttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0196Sequence assemblyWindowsLinuxMacC++GPL-3.0EmergingFree of chargehttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_3218Sequencing quality controlPicoporeReduce the size of Oxford Nanopore Technologies' datasets without losing information.https://github.com/scottgigante/picoporepicoporebiotools:picopore1.2.0Libraryhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622GenomicsWindowsLinuxMacPythonGPL-3.0BiocondaPython Software Foundationhttps://anaconda.org/bioconda/picoporeRepositoryBioconda packagehttps://pypi.org/project/picopore/RepositoryPython Software Foundation10.12688/f1000research.11022.1PrimaryScott GigantePersonPrimary contactSLiMEvolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.https://messerlab.org/slim/SLiM_softwarebiotools:SLiM_software5.2Command-line toolDesktop applicationhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3299Evolutionary biologyWindowsLinuxMacC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0230Sequence generationhttp://edamontology.org/operation_0550DNA substitution modellinghttp://edamontology.org/operation_3946Ecological modellingRun individual-based eco-evolutionary simulations with explicit geneticshttps://messerlab.org/slim/Software catalogueSLiM home page in the Messer Lab websitehttps://github.com/MesserLab/SLiMRepositoryGitHub repository for SLiMhttps://groups.google.com/g/slim-discussDiscussion forumDiscussion forum for SLiM questionshttps://groups.google.com/g/slim-announceMailing listAnnouncements mailing listhttp://benhaller.com/slim/SLiM.zipSource codeA source archive for the command-line `slim` tool only. Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.https://github.com/MesserLab/SLiM/releases/latestDownloads pageThe GitHub page for the current release version, to obtain full source code.http://benhaller.com/slim/SLiM_Manual.pdfUser manualThe manual for SLiM itselfhttp://benhaller.com/slim/Eidos_Manual.pdfUser manualThe manual for Eidos, the scripting language used by SLiMhttp://benhaller.com/slim/SLiMEidosRefSheets.zipQuick start guideQuick reference sheets for SLiM and Eidos10.1093/molbev/msy22830517680PMC6389312Primary3.0B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.10.1093/molbev/msy23730590560PMC6501880Method3.0B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.10.1111/1755-0998.1296830565882PMC6393187Primary3.0B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.10.1101/2025.08.07.66915540832315PMC12363870Primary5.0BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.66915510.1086/72360137130229PMC10793872Primary4.0B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.Philipp Messermesser@cornell.eduhttps://messerlab.orghttps://orcid.org/0000-0001-8453-9377PersonPrimary contactBenjamin C. Hallerbhaller@benhaller.comhttp://benhaller.comhttps://orcid.org/0000-0003-1874-8327PersonPrimary contactPROVEANA software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.http://provean.jcvi.org/index.phpproveanbiotools:proveanWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3120Protein variantsLinuxWindowsMacShellGPL-3.0Animal and Crop Genomicshttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_3197Genetic variation analysishttp://provean.jcvi.org/index.phpGeneral10.1371/journal.pone.004668823056405PMC3466303Primaryhttp://provean.jcvi.org/contact.phpPersonPrimary contactquacQuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES samples and then summarizes their results using pre-defined, configurable QC thresholds.https://github.com/uab-cgds-worthey/quacquacbiotools:quac2.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysisPythonGPL-3.0SequencingMatureFree of chargeOpen accesshttp://edamontology.org/operation_3218Sequencing quality controlhttps://github.com/uab-cgds-worthey/quacRepositoryhttps://github.com/uab-cgds-worthey/quac/releases/tag/2.0Source code2.0https://quac.readthedocs.io/General10.21105/joss.05313Manavalan Gajapathyhttps://github.com/ManavalanGhttps://orcid.org/0000-0002-8606-0113PersonPrimary contactRosalutionRosalution 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)

http://edamontology.org/data_0958Tool metadatahttp://edamontology.org/format_3750YAMLhttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_2332XML

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.htmlPersonRhizoVision 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 contactFreezing-PointFreezing-Point is a user-friendly open-source software for the automated analysis of freezing behavior in rodents. Based on recorded videos or pose estimation files. An adaptive, data-driven algorithm automatically determines freezing detection thresholds, reducing subjective bias while preserving user oversight. Freezing-Point adopts a user-oriented design centered on a graphical interface that provides continuous visual access to original data, processing steps and analysis results. This design enables users to inspect, validate or refine results while minimizing unnecessary data manipulation.https://github.com/gillescourtand/Freezing-PointFreezing-Pointbiotools:Freezing-Point1.0.2Desktop applicationhttp://edamontology.org/topic_3304NeurobiologyMacLinuxWindowsPythonGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2425Optimisation and refinementhttps://github.com/gillescourtand/Freezing-Point/releasesBinaries1.0.2https://github.com/gillescourtand/Freezing-Point/blob/main/Doc/User_guide.mdQuick start guideWEBnmaWEBnm@ 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_1476PDB

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3508PDF

http://edamontology.org/data_1354Sequence profilehttp://edamontology.org/format_2330Textual format

Constructs 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_1476PDB

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3508PDF

http://edamontology.org/data_0889Structural profilehttp://edamontology.org/format_2330Textual format

Performs 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, NorwayInstituteProviderUiBInstituteProviderBioMercatorBioMercator is a software that provides a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis, graphical representation of large datasets. User may import sequence and genome annotations datasets within the software in order to display functional annotation related to QTL and meta-QTL.https://sourcesup.renater.fr/projects/biomercatorBioMercatorbiotools:BioMercator4.2.3Desktop applicationhttp://edamontology.org/topic_3055Quantitative geneticshttp://edamontology.org/topic_0780Plant biologyLinuxWindowsMacJavaGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_2944Physical mappinghttp://edamontology.org/data_1860QTL maphttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1288Genome maphttp://edamontology.org/format_1975GFF3https://sourcesup.renater.fr/frs/?group_id=2301Binaries4.2.310.1093/bioinformatics/bth230150598203BigSeqKitThe Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx.https://github.com/citiususc/BigSeqKitbigseqkitbiotools:bigseqkitLibraryCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxPythonGPL-3.0http://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0372DNA transcriptionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

PLASTPLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a "seed-and-extend approach" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.https://github.com/tischulz1/plastpangenome-blastbiotools:pangenome-blast0.0.1-0.2.0Command-line toolhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0080Sequence analysisLinuxMacWindowsC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1211unambiguous pure nucleotidehttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_3975GFA 1http://edamontology.org/format_2333Binary format

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_1333BLAST results

In order to search for alignments within the pangenome graph, A pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software "Bifrost" and (3) a program-specific index data structure in binary format.PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLinehttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_3975GFA 1http://edamontology.org/format_2333Binary format

If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fastahttps://gitlab.ub.uni-bielefeld.de/gi/plastRepositoryhttps://github.com/tischulz1/plastMirrorhttps://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.mdGeneral10.1093/bioinformatics/btab07733532821PMC8388040PrimaryMethodBenchmarking studyBielefeld Universityhttps://www.uni-bielefeld.de/InstituteProviderGenome Informaticshttps://gi.cebitec.uni-bielefeld.de/InstituteProviderTizian Schulzplast-service@cebitec.uni-bielefeld.dehttps://orcid.org/0000-0003-0744-7078PersonDeveloperESIprotCharge state determination and molecular weight calculation for low resolution electrospray ionization data.https://nube-gran.de/esiprotesiprotbiotools:esiprotWeb applicationDesktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacPythonGPL-3.0ms-utilsProteomicshttp://edamontology.org/operation_0398Protein molecular weight calculationhttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3245Mass spectrometry data format

http://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3245Mass spectrometry data format

http://www.bioprocess.org/esiprot/esiprot_form.phpMirrorhttp://ms-utils.orgSoftware cataloguehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprotGeneral10.1002/rcm.438420049890Robert Winklerrobert.winkler@ira.cinvestav.mxPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorkollaRkollaR is an open-source R library for eye-tracking analysis and visualization, offering functions for event detection, AOI-based analyses, and algorithm comparison. It provides implementations of several algorithms and includes visualizations for data exploration.https://CRAN.R-project.org/package=kollaRkollarbiotools:kollarhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_2815Human biologyRGPL-3.0http://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_0337Visualisation10.3758/S13428-025-02903-Z41361102PMC12685970Johan Lundin Klebergjohan.lundin.kleberg@su.sePersonProAEProAE is an R package and collection of SAS macros designed for standardized analysis and graphical representation of patient-reported outcomes and adverse events data, specifically focusing on PRO-CTCAE.https://duecklab.github.io/proae.htmlproaebiotools:proaehttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3068Literature and languageRGPL-3.0http://edamontology.org/operation_3435Standardisation and normalisationhttps://CRAN.R-project.org/package=ProAERepository10.1186/S12911-025-03320-041422214Amylou C Dueckdueck.amylou@mayo.eduPersonPv3RsPv3Rs is an R package that allows users to infer the cause (recrudescence, relapse, or reinfection) of Plasmodium vivax malaria recurrence using genetic data. It implements a statistical model to compute posterior probabilities of recurrence states and is freely available on CRAN under the GNU license.https://cran.r-project.org/web/packages/Pv3Rs/index.htmlpv3rsbiotools:pv3rshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3305Public health and epidemiologyRGPL-3.0http://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_0337Visualisation10.1093/BIOINFORMATICS/BTAF64341324557PMC12758599Aimee R Tayloraimee.taylor@pasteur.frPersonPSQANPSQAN is a Snakemake and R workflow designed to prioritize high-confidence and biologically relevant transcripts from long-read RNA sequencing data, facilitating the interpretation of transcript characterization results.https://github.com/sid-sethi/PSQANpsqanbiotools:psqanhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0769WorkflowsRGPL-3.0http://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_0337Visualisation10.1093/BIOADV/VBAF29341394080PMC12701792Siddharth Sethisiddharth.sethi@astx.comhttps://orcid.org/0000-0002-4398-4295PersonMina Rytenmr2022@medschl.cam.ac.ukhttps://orcid.org/0000-0001-9520-6957PersonRISKRISK is a tool for biological network annotation and visualization that integrates community detection algorithms and overrepresentation analysis. It supports diverse network types and generates publication-ready visualizations, demonstrating scalability and adaptability for modern network analysis.https://github.com/riskportal/riskriskbiotools:riskhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3318Physicshttp://edamontology.org/topic_2269Statistics and probabilityPythonGPL-3.0http://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_3501Enrichment analysis10.1093/BIOINFORMATICS/BTAF66941423796PMC12766918Hannes Rösthannes.rost@utoronto.cahttps://orcid.org/0000-0003-0990-7488PersonWatConWatCon is a Python package for analyzing conserved water networks across protein families using both dynamic and static structural information. It enables classification of water network conservation, characterization of water networks, and projection of results for visual interpretation.https://watcon.readthedocs.iowatconbiotools:watconhttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0593NMRhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0154Small moleculesPythonGPL-3.0http://edamontology.org/operation_0387Molecular surface calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0321Protein structure validation10.1021/JACSAU.5C0044741450622PMC12728608Shina C. L. Kamerlinskamerlin3@gatech.eduhttps://orcid.org/0000-0002-3190-1173Personcrm12Combcrm12Comb is an R package that implements adaptive designs for integrated phase I/II trials of drug combinations using the Continual Reassessment Method (CRM). It enables patient assignment guidance and simulation studies for evaluating toxicity and efficacy, providing flexibility for diverse clinical scenarios.https://cran.r-project.org/web/packages/crm12Comb/crm12combbiotools:crm12combhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_0209Medicinal chemistryhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3373Drug developmenthttp://edamontology.org/topic_3377Safety sciencesRGPL-3.0http://edamontology.org/operation_4009Small molecule designhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3454Phasing10.1371/JOURNAL.PONE.033614641212869PMC12599976Song Wusong.wu@stonybrook.eduPersonJie Yangjie.yang@stonybrookmedicine.eduhttps://orcid.org/0000-0003-3469-5931PersonstPipestPipe is an R/Bioconductor pipeline designed for preprocessing sequencing-based spatial transcriptomics data, offering a flexible and streamlined workflow for tasks like FASTQ trimming and gene count matrix generation.https://bioconductor.org/packages/stPipestpipebiotools:stpipehttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0102MappingRGPL-3.0http://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/operation_3933Demultiplexinghttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0335Data formatting10.1093/NARGAB/LQAF16741278534PMC12639247Yang Xuxu.ya@wehi.edu.auPersonMatthew E Ritchiemritchie@wehi.edu.auhttps://orcid.org/0000-0002-7383-0609PersonoligoN-designoligoN-design is a versatile tool for designing specific oligonucleotide probes and primers from large datasets, particularly useful for ecological and evolutionary studies relying on PCR or FISH. It's easily installed via bioconda and simplifies the design process for high-throughput sequencing data analyses.http://bioconda.github.io/recipes/oligon-design/README.htmloligon-designbiotools:oligon-designhttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3519PCR experimentGPL-3.0http://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_3198Read mapping10.1101/2025.11.04.685038Miguel M. SandinPersonSISTEMSISTEM is a software package for simulating tumor evolution and cell migrations at single-cell resolution, allowing for genotype-driven selection and generation of realistic DNA sequencing data.https://github.com/samsonweiner/sistemsistembiotools:sistemhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3315MathematicsPythonGPL-3.0http://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3446Cell migration analysishttp://edamontology.org/operation_3196Genotyping10.1093/BIOINFORMATICS/BTAF63441275416PMC12701798Mukul S Bansalmukul.bansal@uconn.eduhttps://orcid.org/0000-0003-0039-2596Personmethodicalmethodical is a Bioconductor package that identifies genomic regions where DNA methylation is correlated with transcription, revealing transcript-proximal methylation-associated regulatory sites (TMRs). It combines RNA-seq and whole genome bisulfite sequencing (WGBS) data to refine regulatory logic in normal and tumor tissues.https://bioconductor.org/packages/methodicalmethodicalbiotools:methodicalhttp://edamontology.org/topic_3674Methylated DNA immunoprecipitationhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_3512Gene transcriptsRGPL-3.0http://edamontology.org/operation_0417Post-translational modification site predictionhttp://edamontology.org/operation_3919Methylation callinghttp://edamontology.org/operation_0440Promoter predictionhttp://edamontology.org/operation_0372DNA transcriptionhttp://edamontology.org/operation_3207Gene methylation analysis10.1093/NAR/GKAF94941036619PMC12481017Richard Heeryrichardheery@gmail.comPersonMartin H Schaefermartin.schaefer@ieo.ithttps://orcid.org/0000-0001-7503-6364Personsvycdiffsvycdiff is an R package designed for estimating controlled differences in complex survey data, particularly for health disparities research. It offers methods for estimating population average controlled differences and is tailored for surveys with complex sampling designs.http://cran.r-project.org/web/packages/svycdiff/svycdiffbiotools:svycdiffhttp://edamontology.org/topic_3390Nutritional sciencehttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_2269Statistics and probabilityRGPL-3.0http://edamontology.org/operation_3432Clustering10.1002/SIM.7028941055541PMC12636266FLAMESv2FLAMESv2 is an R/Bioconductor package for analyzing long-read single-cell RNA-seq data, supporting isoform detection, annotation, and analysis with automated pipelines and customizable functions. It facilitates comprehensive analysis for diverse experimental protocols and provides visualization and analysis outputs.https://bioconductor.org/packages/FLAMESflamesv2biotools:flamesv2http://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_4028Single-cell sequencinghttp://edamontology.org/topic_0769WorkflowsRGPL-3.0http://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_3680RNA-Seq analysishttps://sefi196.github.io/FLAMESv2_LR_sc_tutorial/Training material10.1101/2025.10.19.683327rtPCRrtPCR is an R package for statistical analysis and graphical presentation of qPCR data. It provides tools for data analysis, including t-tests, ANOVA, and ANCOVA, along with publication-ready visualizations.https://cran.r-project.org/web/packages/rtpcr/index.htmlrtpcrbiotools:rtpcrhttp://edamontology.org/topic_3519PCR experimenthttp://edamontology.org/topic_3452Tomographyhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0632Probes and primersGPL-3.0http://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0337Visualisation10.7717/PEERJ.2018541112768PMC12530193Ghader Mirzaghaderimirzaghaderi@gmail.comPersonxCell2xCell2 is a tool for cell type enrichment analysis using cell type signatures, offering training capabilities and lineage identification features. It predicts response to immune checkpoint blockade and includes pre-trained references for various datasets.https://dviraran.github.io/xCell2refsxcell_20biotools:xcell_20http://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3518Microarray experimentRGPL-3.0http://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttps://bioconductor.org/packages/xCell2Repository10.1186/S13059-025-03784-341044684PMC12492622Dvir Arandviraran@technion.ac.ilPersonminamina is an R package that integrates diversity and network analyses to study microbial communities. It allows for network comparison and identification of condition-specific interactions, providing deeper insights into community ecology.https://bioconductor.org/packages/release/bioc/html/mina.htmlminabiotools:minahttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3810Agricultural scienceRGPL-3.0http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/operation_3891Essential dynamics10.1128/MSYSTEMS.00564-2540952002PMC12542658Rui Guanrg684@cam.ac.ukhttps://orcid.org/0000-0003-0862-2368PersonRuben Garrido-Otergarridoo@mpipz.mpg.dehttps://orcid.org/0000-0003-1769-892XPersonMotilAMotilA is a Python pipeline for quantifying microglial fine process motility from 3D time-lapse microscopy data. It performs image preprocessing, segmentation, and motility quantification, yielding biologically interpretable metrics and is suitable for various imaging applications.https://github.com/FabrizioMusacchio/motilamotilabiotools:motilahttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_2229Cell biologyPythonGPL-3.0http://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3443Image analysis10.1101/2025.08.04.668426IsoBayesIsoBayes is a Bayesian method for single-isoform proteomics inference, integrating mass spectrometry proteomics and transcriptomics data. The software is available as a Bioconductor R package and accompanied by an example usage vignette.https://figshare.com/projects/IsoBayes_paper_data/183988isobayesbiotools:isobayeshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3520Proteomics experimentRGPL-3.0http://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3767Protein identificationhttps://bioconductor.org/packages/IsoBayesRepository10.1093/BIOINFORMATICS/BTAF45040796134PMC12377908Gloria M Sheynkmanhttps://orcid.org/0000-0002-4223-9947PersonSimone Tiberisimone.tiberi@unibo.ithttps://orcid.org/0000-0002-3054-9964PersonfuseMLRfuseMLR is an R package for integrative prediction modeling of multi-omics data, enabling modality-specific variable selection and prediction modeling followed by aggregation into a final meta-model. It facilitates a systematic and reproducible approach to late integration predictive modeling.https://cran.r-project.org/web/packages/fuseMLRfusemlrbiotools:fusemlrhttp://edamontology.org/topic_4021Multiomicshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3577Personalised medicineRGPL-3.0http://edamontology.org/operation_3557Imputationhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_3936Feature selection10.1186/S12859-025-06248-440859122PMC12382258Césaire J. K. Fouodocesaire.kuetefouodo@uni-luebeck.dePersonSilke Szymczaksilke.szymczak@uni-luebeck.dePersonRQdeltaCTRQdeltaCT 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.plPersonStatialStatial is an R package on Bioconductor that identifies changes in cell state relative to spatial associations, quantifying the impact of spatial proximity on cell phenotype and uncovering changes in marker expression associated with varying levels of localisation.https://bioconductor.org/packages/release/bioc/html/Statial.htmlstatialbiotools:statialhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0080Sequence analysisRGPL-3.0http://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3659Regression analysis10.1093/BIOINFORMATICS/BTAF40940674581PMC12343047Ellis Patrickellis.patrick@sydney.edu.auhttps://orcid.org/0000-0002-5253-4747Person2dSpAn-Auto2dSpAn-Auto is a software tool for automated analysis of two-dimensional dendritic spine images, offering modality-agnostic spine segmentation based on 2D skeletonization with both binary and fuzzy skeletonization workflows.https://github.com/CMATERJU-BIOINFO/2dSpAn-Auto2dspan-autobiotools:2dspan-autohttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3334Neurologyhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3500ZoologyGPL-3.0http://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3799Quantification10.1186/S12859-025-06179-040597607PMC12211165Subhadip Basusubhadip.basu@jadavpuruniversity.inPersonJakub Wlodarczykj.wlodarczyk@nencki.edu.plPersoncytoKernelcytoKernel is an R package implementing a kernel-based score test for differential expression analysis of single-cell data, designed to detect subtle variations often missed by traditional methods. It’s available from Bioconductor and offers comprehensive documentation and installation options.http://bioconductor.org/packages/cytoKernelcytokernelbiotools:cytokernelhttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_4028Single-cell sequencinghttp://edamontology.org/topic_0121ProteomicsRGPL-3.0http://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0337Visualisation10.1093/BIOINFORMATICS/BTAF39940658464PMC12312792Tusharkanti Ghoshtusharkanti.ghosh@cuanschutz.eduhttps://orcid.org/0000-0002-7537-6374PersonscGOclustscGOclust is an R package that leverages Gene Ontology (GO) terms to compare cell type functional profiles across and within species, even when phylogenetically distant. It facilitates the discovery of functionally analogous cell types by constructing de novo cellular functional profiles using GO terms.https://cran.r-project.org/web/packages/scGOclust/index.htmlscgoclustbiotools:scgoclusthttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3500ZoologyRGPL-3.0http://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_0313Expression profile clusteringhttp://edamontology.org/operation_3352Ontology comparisonhttp://edamontology.org/operation_3891Essential dynamics10.1093/BIOINFORMATICS/BTAF19540662793PMC12261464Yuyao Songysong@ebi.ac.ukhttps://orcid.org/0000-0001-9738-9726PersonIrene Papatheodorouirene.papatheodorou@earlham.ac.ukhttps://orcid.org/0000-0001-7270-5470PersonColorI-DTColorI-DT is an open-source MATLAB tool for quantitatively evaluating differences in microscopy color images, providing a user-friendly means of assessing color variation using various metrics.https://sourceforge.net/p/colori-dt/icolori-dtbiotools:icolori-dthttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3315MathematicsGPL-3.0http://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3552Microscope image visualisationhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3891Essential dynamics10.1016/J.CSBJ.2025.06.01940574786PMC12197881Filippo Piccininifilippo.piccinini@irst.emr.itPersonMDSvisMDSvis is a Shiny application for visualizing Multi Dimensional Scaling (MDS) projections. It leverages the CytoMDS package for calculating MDS coordinates and allows users to interactively customize plots through a GUI.http://uclouvain-cbio.github.io/MDSvismdsvisbiotools:mdsvishttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3372Software engineeringRGPL-3.0http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_3891Essential dynamics10.1101/2025.06.23.660991PhyClonePhyClone is a software resource that accurately reconstructs cancer phylogenies from bulk sequencing data using a probabilistic model. It is available on GitHub and can be installed via Bioconda.https://github.com/Roth-Lab/PhyClonephyclonebiotools:phyclonehttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_0199Genetic variationGPL-3.0http://edamontology.org/operation_3625Relation extraction10.1093/BIOINFORMATICS/BTAF34440511985MAFcounterMAFcounter is a tool for counting k-mers in Multiple Alignment Format (MAF) files, designed to address a previously unmet need in bioinformatics. The software is multithreaded, fast, and memory efficient, making it suitable for large-scale sequence alignment analysis.https://github.com/Georgakopoulos-Soares-lab/MAFcountermafcounterbiotools:mafcounterhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0081Structure analysisC++GPL-3.0http://edamontology.org/operation_3182Genome alignmenthttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysis10.1186/S12859-025-06172-740448014PMC12125892Ioannis Mouratidisioannis.mouratidis@psu.eduPersonIlias Georgakopoulos-Soaresizg5139@psu.eduPersonLTFHPlusLTFHPlus is an R package implementing an extension of the liability threshold family history (LT-FH) model for automatic detection of n-degree family members. It uses a Gibbs sampler and allows for flexible family structures, facilitating analysis of familial aggregation of diseases and traits.https://cran.r-project.org/web/packages/LTFHPlus/index.htmlltfhplusbiotools:ltfhplushttp://edamontology.org/topic_3337Biobankhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0625Genotype and phenotypeRGPL-3.0http://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0337Visualisation10.1101/2025.05.16.25327749Emil M. PedersenPersonSOMMDSOMMD is an R package that streamlines the analysis of molecular dynamics simulations using self-organizing maps. It offers tools for importing data, generating visualizations, and reconstructing transition networks.https://CRAN.R-project.org/package=SOMMDsommdbiotools:sommdhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0769WorkflowsRGPL-3.0http://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/operation_0533Expression profile pathway mappinghttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_2476Molecular dynamics10.1093/BIOINFORMATICS/BTAF30840372445PMC12187059Stefano Mottastefano.motta@unimib.ithttps://orcid.org/0000-0002-0812-6834PersonAlessandro Pandinialessandro.pandini@brunel.ac.ukhttps://orcid.org/0000-0002-4158-233XPersonrPIMSrPIMS is a Shiny R package designed to simplify breed identification and genetic analysis in livestock using genomic data and machine learning approaches. It provides modules for data input, dimensionality reduction, phylogenetic tree construction, population structure analysis, and machine learning-based classification.https://github.com/Werewolfzy/rPIMSrpimsbiotools:rpimshttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_3500Zoologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_2885DNA polymorphismRGPL-3.0http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0324Phylogenetic analysishttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3935Dimensionality reduction10.1093/BIOADV/VBAF07740330626PMC12052404Lin Jiangjianglin@caas.cnhttps://orcid.org/0000-0001-9123-5988Person