Phylo-MoviesPhylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.https://enesberksakalli.github.io/phylo-movies/phylo-moviesbiotools:phylo-movies0.98.1Desktop applicationWeb applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0092Data visualisationWindowsMacLinuxPythonJavaScriptTypeScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/format_3464JSON

Visualizes ordered phylogenetic tree series as animated transition movies with comparison, MSA context, movement analytics, image export, and recording support.https://github.com/enesBerkSakalli/phylo-moviesRepositorySource code repository.https://enesberksakalli.github.io/phylo-movies/demo/ServiceStatic browser demo with precomputed example movies.https://github.com/enesBerkSakalli/phylo-movies/issuesIssue trackerhttps://github.com/enesBerkSakalli/phylo-moviesSource codeSource checkout for full web application and backend workflows.0.98.1https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1BinariesDesktop convenience builds for macOS, Windows, and Linux.0.98.1https://enesberksakalli.github.io/phylo-movies/manual/User manualResearcher-facing manual.https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.mdGeneralProject overview, installation, usage, citation, and links.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.mdInstallation instructionsLocal source-checkout setup instructions.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.mdAPI documentationBackend API documentation.10.64898/2026.04.01.715821PrimarybioRxiv preprint describing the Phylo-Movies method and examples.10.5281/zenodo.20488923Primary0.98.1Archived software release on Zenodo.Enes Berk Sakallienes@lbi-netmed.athttps://github.com/enesBerkSakalliPersonDeveloperPrimary contactCorresponding software contact.Simon E. HaendelerPersonDeveloperArndt von HaeselerPersonDeveloperHeiko A. SchmidtPersonDeveloperMicroMinerMicroMiner assists in identifying single-residue substitutions in protein structure databases. It searches protein residue environments with local sequence and structural similarity based on the SIENA methodology. Users can search for structural mutation in the entire PDB, their in-house structure collection, or (subsets of) the AlphaFold Database. They can use the method to explore the mutation landscape of proteins with experimental or predicted structures. MicroMiner can be applied to single domains or even protein-protein or protein-ligand interfaces. Several filter options to simplify downstream analysis are available.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/microminer.htmlmicrominerbiotools:microminerCommand-line toolWeb servicehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091BioinformaticsMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1497Root-mean-square deviation

http://edamontology.org/data_1481Protein structure alignmenthttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_2330Textual format

structural single-residue substitution search and analysishttps://proteins.plusServiceA web service to run MicroMiner calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralsienauses10.1093/bib/bbad357Primaryproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service Issuessoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderJAMDAJAMDA enables the preparation of individual protein structures and the docking of small molecules in preprocessed binding sites of choice. JAMDA simplifies the process of protein-ligand docking by automatic preprocessing protocols for the protein and binding sites of interest. The JAMDAscore scoring function retrieved 75% of the native poses in the three highest-ranked solutions for high-quality protein-ligand complexes with default settings. Individual configurations for protein preparation are available, e.g., considering protein ensembles, relevant binding site water molecules, or cofactors. A user-defined number of input conformations for the ligands of interest can be generated fully automated using Conformator. Alternatively, users can also provide externally prepared ligand conformers.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/jamda.htmljamdabiotools:jamdaWeb serviceCommand-line toolhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0082Structure predictionWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3816Mol2http://edamontology.org/format_3814SDFhttp://edamontology.org/format_1197InChIhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_3752CSV

http://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1772Score

http://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1497Root-mean-square deviation

protein-ligand docking for small moleculeshttps://proteins.plusServiceA web service to run JAMDA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralprotossuses10.1021/acs.jcim.3c01573Primary10.1002/jcc.26522Method10.1021/acs.jcim.0c01095MethodProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderStructureProfilerThree-dimensional protein structures play a vital role in drug design. Structure-based design necessitates an in-depth examination of the available quality data before using the structure in computational experiments and for method evaluation. StructureProfiler assists in automatically profiling sets of protein-ligand complex structures based on multiple quality indicators, ranging from model characteristics, e.g., the R factor, and active site features, e.g., bond length deviations, to ligand properties such as electron density support and the validity of torsion angles.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/structureprofiler.htmlStructureProfilerbiotools:StructureProfilerWeb serviceWeb APICommand-line toolhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3572Data quality managementhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_1317Structural biologyLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_1844Protein geometry validationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1539Protein structural quality report

http://edamontology.org/data_2991Protein geometry data

quality profiling for protein-ligand complexeshttps://proteins.plusServiceA web service to run StructureProfiler calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/structurechecker_restServiceA web API to run StructureProfiler calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneral10.1093/bioinformatics/bty69230124779PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderWarPPWarPP predicts the position and orientation of water molecules in small-molecule binding sites. It places and scores water molecules in binding sites of crystallographic structures based on EDIAscorer results and interaction geometries as known from experimentally solved protein structures. WarPP was validated on a high-quality set of 1,500 protein-ligand complexes, containing 20,000 crystallographically observed water molecules. It is sufficiently fast for high-throughput analyses. It correctly places water molecules in approx. 80% of the cases. Users can export the predictions as PDB files for, e.g., molecular docking with JAMDA.https://www.zbh.uni-hamburg.de/forschung/amd/software/warpp.htmlwarppbiotools:warppCommand-line toolWeb APIWeb servicehttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual format

water molecule placementhttps://proteins.plusServiceA web service to run WarPP calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/warpp_restServiceA web API to run WarPP calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneral10.1021/acs.jcim.8b0027130036062PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderLifeSoaksLifeSoaks was designed to find solvent channels in macromolecular structures solved by X-ray crystallography. It predicts their accessibility by molecules through an automated annotation of so-called bottleneck radii. It simplifies the process of manually checking a crystal structure for solvent channels. Bottleneck radii can be calculated for solvent channels and small molecule binding sites. The tool is ideally suited for channel analyses before the actual soaking experiments to select the most promising experimental conditions and crystal forms. LifeSoaks runs fully automated and will finish within seconds to minutes for moderately sized crystals.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/lifesoaks.htmllifesoaksbiotools:lifesoaksWeb serviceCommand-line toolhttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0091BioinformaticsWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2019Map data

http://edamontology.org/data_1542Protein solvent accessibility

calculating bottleneck radii for crystal solvent channelshttps://proteins.plusServiceA web service to run LifeSoaks calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomi.deSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneral10.1107/S205979832300582XPrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderEDIAscorerThe electron density score for individual atoms (EDIA) quantifies the electron density fit of each atom in a crystallographically resolved structure. Multiple EDIA values can be combined using the power mean to compute the EDIAm, i.e., the electron density score for a group of several atoms. It enables users to score a set of atoms, such as a ligand, a residue, or an active site.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.htmlediabiotools:ediaWeb serviceCommand-line toolWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellingWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1772Score

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2019Map data

atom-level assessment of the electron density fit for structures solved by X-ray crystallographyhttps://proteins.plusServiceA web service to run EDIAscorer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/edia_restServiceA web API to run EDIAscorer calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneralstructureprofilerusedBy10.1021/acs.jcim.7b0039128981269PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.deSupportNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.deSupportUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderSIENASIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/siena.htmlsienabiotools:sienaWeb serviceWeb APICommand-line toolhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionsLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1384Sequence alignment (protein)

http://edamontology.org/data_1497Root-mean-square deviation

http://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1481Protein structure alignmenthttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_2330Textual format

PDB mining and protein binding site ensemble generationhttps://proteins.plusServiceA web service to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://proteins.plus/help/siena_restServiceA web API to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralproteinsplusincludedIn10.1021/acs.jcim.5b0058826759067MethodPrimary10.1021/acs.jcim.5b0021026098831MethodProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderDoGSite3DoGSite3 was developed for predicting robust and reliable small molecule binding sites and computing their geometrical and chemical descriptors. It is based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets. The new tool is largely rotation- and translation-invariant due to a normalization procedure before binding site prediction. Known ligands in the structure can be used to bias the grid by sufficiently buried ligand fragments. The output encompasses novel chemical binding site descriptors considering solvent accessibility. Compared to its predecessor, it shows increased robustness through comprehensive parameter optimization. DoGSite3 runs finish within seconds.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsite3.htmldogsite3biotools:dogsite3Command-line toolWeb APIWeb servicehttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0123Protein propertiesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2019Map data

small molecule binding site detectionhttps://proteins.plusServiceA web service to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/dogsite3_restServiceA web API to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralgeomineusedBy10.1021/acs.jcim.3c0033637130052PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderFrameXploreFrameXplore is a Google Colab notebook that extends ColabFold to automatically identify and correct disulfide bonds in cysteine‑rich protein structures. After a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and provides an interactive 3D view.https://github.com/Vidhusv/FRAMEXPLORERframexplorebiotools:framexplore1.0.0doi:10.5281/zenodo.20135079doiWeb applicationhttp://edamontology.org/topic_4019BiosciencesLinuxMacWindowsPythonMITEmergingFree of chargeOpen accesshttps://github.com/Vidhusv/FRAMEXPLORERRepositoryGitHub repository with source code, documentation, and logohttps://github.com/Vidhusv/FRAMEXPLORER/issuesIssue trackerReport bugs, suggest features, or ask questionshttps://github.com/Vidhusv/FRAMEXPLORER/archive/refs/heads/main.zipSource codeLatest version of the complete repository as a ZIP file1.0.0https://raw.githubusercontent.com/Vidhusv/FRAMEXPLORER/main/FrameXplore.ipynbBinariesDirect download of the Colab notebook (.ipynb file). Can be run locally or uploaded to Google Colab.1.0.0https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.mdGeneralQuick start guide, example test case, methodology explanation, citation, and repository contents10.1038/s41592-022-01488-135637307PMC9184281PrimaryColabFold: making protein folding accessible to all. Nature Methods, 2022.Vidhu S Vijayvidhuvijay2003@gmail.comhttps://github.com/Vidhusvhttps://orcid.org/0009-0009-1182-2089PersonDeveloperMaintainerMS Bioinformatics student at Amrita Vishwa Vidyapeetham; creator and maintainer of FrameXplore.pathotyprA fast, offline, pathogen-agnostic toolkit for lineage classification and marker-driven genotyping from whole-genome sequencing data. Bring your own SNP marker panel for any microbial pathogen — pathotypr handles the rest. Ships with curated panels for Mycobacterium tuberculosis complex (MTBC): 3,707 lineage-defining SNPs and over 102,000 resistance-associated mutations. Works with assembled genomes (FASTA) and raw reads (FASTQ). Available as command-line interface and cross-platform desktop GUI (Tauri).https://github.com/PathoGenOmics-Lab/pathotyprpathotyprbiotools:pathotypr1.0.0Command-line toolDesktop applicationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_3474Machine learningRustAGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3475TSV

train — Build a Random Forest classifier from labeled genomes.http://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3475TSV

predict — Assign lineages to genomes using a pre-trained Random Forest model.http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3475TSV

classify — Call known SNP markers in assembled genomes against a user-defined marker panel.http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3475TSV

split-fastq — Alignment-free genotyping directly from raw reads using k-mer matching.http://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3475TSV

match — Find the closest reference genome from a set of references for raw reads.https://github.com/PathoGenOmics-Lab/pathotypr/releasesBinarieshttps://github.com/PathoGenOmics-Lab/pathotyprSource codehttps://github.com/PathoGenOmics-Lab/pathotypr/tree/main/docsUser manual10.64898/2026.03.24.714002PrimaryPaula Ruiz-Rodriguezhttps://orcid.org/0000-0003-0727-5974PersonDeveloperMaintainerMireia Coscollahttps://orcid.org/0000-0003-0752-0538PersonPrimary contactI2SysBio (CSIC - Universitat de València)InstituteProviderPathoGenOmics LabDivisionProviderCOPASIOpen-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. It includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.http://copasi.org/copasibiotools:copasiCommand-line toolLibraryDesktop applicationhttp://edamontology.org/topic_2259Systems biologyMacLinuxWindowsC++Artistic-2.0de.NBIEBI Training ToolsMatureFree of chargeOpen accessGermanyhttp://edamontology.org/operation_3562Network simulationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3926Pathway visualisationhttp://edamontology.org/operation_3660Metabolic network modellinghttp://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3686COMBINE OMEXhttp://edamontology.org/format_3685SED-MLhttp://edamontology.org/format_3239CopasiMLhttp://edamontology.org/format_2585SBML

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3686COMBINE OMEXhttp://edamontology.org/format_3685SED-MLhttp://edamontology.org/format_3239CopasiMLhttp://edamontology.org/format_2585SBML

https://groups.google.com/g/copasi-user-forumDiscussion forumUser Forumhttp://tracker.copasi.org/Issue trackerIssue trackerhttps://github.com/copasi/COPASIRepositoryGithub Repohttps://fosstodon.org/@copasiSocial mediahttp://copasi.org/Download/BinariesSource and binary packages are available for download.http://copasi.org/Support/User_Manual/User manualcorcusedBypycotoolsusedBybiosimulationsincludedInsbmlwebappusedBylibsbmlusesbasicousedBy10.1093/bioinformatics/btl4851703268310.1007/978-1-59745-525-1_21939943310.1016/j.jbiotec.2017.06.120028655634PMC5623632http://copasi.org/About/Team/PersonPrimary contactFrank T. Bergmannfrank.bergmann@bioquant.uni-heidelberg.dehttps://orcid.org/0000-0001-5553-4702PersonPrimary 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 guideBioMercatorBioMercator 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/bth230150598203RecGraphRecGraph is a tool for computing optimal sequence-to-graph alignment with recombinations.https://github.com/AlgoLab/RecGraphrecgraphbiotools:recgraph1.0.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3796Population genomicsLinuxMacRustMITEmergingToolsItalyhttps://github.com/AlgoLab/RecGraphRepositoryhttps://github.com/AlgoLab/RecGraph/issuesIssue trackerhttps://github.com/AlgoLab/RecGraph/releases/tag/v1.0.0Binaries1.0.0https://anaconda.org/channels/bioconda/packages/recgraph/overviewSoftware packagehttps://github.com/AlgoLab/RecGraph/blob/main/README.mdGeneral10.1093/bioinformatics/btae292Primary1.0.0JalviewJalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.https://www.jalview.org/Jalviewbiotools:Jalview2.11.5.1Desktop applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsGPL-3.0ELIXIR-UKMatureFree of chargeOpen accessToolsInteroperabilityUKhttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_1938GFF2-seqhttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3311RNAMLhttp://edamontology.org/format_1915Formathttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1939GFF3-seqhttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_1476PDB

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1947GCG MSF

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3466EPShttp://edamontology.org/format_1915Formathttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3603PNG

Other Input formats: AMSA (.amsa); JnetFile (.concise, .jnet); PFAM (.pfam); Substitution matrix (.matrix); Jalview Project File (.jvp); Jalview Feature File (.features, .jvfeatures); Jalview Annotations File (.annotations, .jvannotations); Predicted Aligned Error (PAE) Matrix File (.json) ... Other Output formats: PFAM (.pfam); BioJS (.biojs) (interactive HTML/Javascript); Jalview Project File (.jvp);https://discourse.jalview.org/Discussion forumhttps://issues.jalview.org/Issue trackerhttps://www.jalview.org/development/jalview_develop/OtherLatest development versionhttps://gitlab.jalview.org/jalview/jalview.gitRepositoryhttps://twitter.com/JalviewSocial mediaTwitter feedhttps://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfwSocial mediaYouTube training videoshttps://www.linkedin.com/company/104771886/Social mediahttps://www.jalview.org/downloadDownloads pagehttps://www.jalview.org/download/source/Source codehttps://www.jalview.org/download/?os=allBinariesBinaries for all platformshttps://www.jalview.org/favicon.svgIconhttps://www.jalview.org/download/other/jar/BinariesExecutable JAR filehttps://www.jalview.org/about/citationCitation instructionshttps://www.jalview.org/training/Training materialHands-on exercises, Training courses and Training videoshttps://www.jalview.org/help/faqFAQhttps://www.jalview.org/help/documentation/User manualjabawsuseschimerauseschimeraxusespymolusesbiocondaincludedIn3d-beaconsusesuniprotusespfamusesensemblusespdbusesrfamuses3d-beaconsuses10.1093/bioinformatics/btp03319151095PMC2672624Jim Procterhttp://www.lifesci.dundee.ac.uk/people/jim-procterhttps://orcid.org/0000-0002-7865-7382PersonPrimary contactGeoff Bartonhttps://www.lifesci.dundee.ac.uk/people/geoff-bartonhttps://orcid.org/0000-0002-9014-5355StripePyStripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoninghttps://github.com/paulsengroup/StripePystripepybiotools:stripepy0.0.10.0.21.0.01.1.01.1.11.2.01.2.11.3.0Command-line toolhttp://edamontology.org/topic_0091BioinformaticsWindowsLinuxMacPythonMIThttps://github.com/paulsengroup/StripePy/issuesIssue trackerhttps://github.com/paulsengroup/StripePy/discussionsDiscussion forumhttps://github.com/paulsengroup/StripePy.gitRepositoryhttps://github.com/paulsengroup/StripePy/releasesSource codehttps://hub.docker.com/r/paulsengroup/stripepyContainer filehttps://doi.org/10.5281/zenodo.14283921Test datahttps://pypi.org/project/stripepy-hic/Binarieshttps://anaconda.org/bioconda/stripepy-hicBinarieshttps://stripepy.readthedocs.io/User manual10.1101/2024.12.20.629789Other10.1093/bioinformatics/btaf351PrimaryhictkpyPython bindings for hictk: read and write .cool and .hic files directly from Pythonhttps://github.com/paulsengroup/hictkpyhictkpybiotools:hictkpy0.0.10.0.20.0.30.0.40.0.51.0.01.1.01.2.01.3.01.4.0Libraryhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacPythonMITMaturehttps://github.com/paulsengroup/hictkpyRepositoryhttps://github.com/paulsengroup/hictkpy/issuesIssue trackerhttps://github.com/paulsengroup/hictkpy/discussionsHelpdeskhttps://github.com/paulsengroup/hictkpy/releasesDownloads pagehttps://pypi.org/project/hictkpy/Binarieshttps://anaconda.org/bioconda/hictkpyBinarieshttps://hictkpy.readthedocs.ioGeneralhttps://hictkpy.readthedocs.io/en/stable/installation.htmlInstallation instructionshttps://hictkpy.readthedocs.io/en/stable/quickstart.htmlQuick start guidehttps://hictkpy.readthedocs.io/en/stable/api/index.htmlAPI documentationhictkuses10.1093/bioinformatics/btae408HBATHBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis of potential hydrogen bonds and similar type of weak interactions in macromolecular structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric approach to identify molecular interactions by analysing distance and angular criteria. HBAT 1.1 was released in 2007 as closed source Windows binary and continue to be available via SourceForge. HBAT 2.0 was introduced in 2025 and a completed rewrite of original implementation with cross-platform support. HBAT 2.0 is open sourced under MIT License.https://hbat.abhishek-tiwari.comhbatbiotools:hbat2.x1.1, 1.0Command-line toolDesktop applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacPerlPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1549Protein hydrogen bonds

hbat input.pdbhttps://github.com/abhishektiwari/hbatRepositoryIssue trackerhttp://www.mybiosoftware.com/hbat-1-1-hydrogen-bond-analysis-tool.htmlSoftware cataloguehttps://pypi.org/project/hbat/Software packageCross-platform PyPI Python Package2.xhttps://github.com/abhishektiwari/hbat/releasesBinariesMac and Linux Binaries including AppImage, .deb, standalone executables.2.xhttps://sourceforge.net/projects/hbat/BinariesWindows Binaries download from SourceForge1.0, 1.1https://hbat.abhishek-tiwari.comGeneralAPI documentationCitation instructionsCommand-line optionsInstallation instructionsQuick start guide10.3233/ISI-2007-0033718467777PrimaryPeer-reviewed paper for HBAT 1.010.5281/zenodo.17645321OtherPreprint for HBAT 2.x softwareAbhishek Tiwarihttps://www.abhishek-tiwari.comhttps://orcid.org/0000-0003-2222-2395PersonPrimary contacthictkBlazing fast toolkit to work with .hic and .cool fileshttps://github.com/paulsengroup/hictkhictkbiotools:hictk1.0.02.0.02.0.12.0.22.1.02.1.12.1.22.1.32.1.42.1.52.2.0Command-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0080Sequence analysisWindowsMacLinuxMITMaturehttps://github.com/paulsengroup/hictkRepositoryhttps://github.com/paulsengroup/hictk/issuesIssue trackerhttps://github.com/paulsengroup/hictk/discussionsHelpdeskhttps://github.com/paulsengroup/hictk/releasesDownloads pagehttps://anaconda.org/bioconda/hictkBinarieshttps://github.com/paulsengroup/hictk/pkgs/container/hictkContainer filehttps://hictk.readthedocs.ioUser manualhictkpyusedByhictkrusedBy10.1093/bioinformatics/btae408PrimaryEl-MAVENFast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.https://github.com/ElucidataInc/ElMavenEl-MAVENbiotools:El-MAVENDesktop applicationhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxWindowsMacGPL-2.0MatureFree of chargeOpen accesshttps://github.com/ElucidataInc/ElMavenRepositoryhttps://github.com/ElucidataInc/ElMaven/issuesIssue trackerhttps://elucidatainc.github.io/ElMaven/Downloads/Binarieshttps://github.com/ElucidataInc/ElMaven/releasesSource codehttps://elucidatainc.github.io/ElMaven/documentation/User manual10.1007/978-1-4939-9236-2_1931119671Primaryinfo@elucidata.ioSupportelmaven@elucidata.ioPersonPrimary contactTiSimTiSim-CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multicellular systems in two and three dimensions. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multicellular phenotypes.https://www.hoehme.com/software/tisimcellsysbiotools:cellsys5.0http://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0621Model organismsPerMedCoEOpen access (with restrictions)http://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/data_3869Simulationhttps://www.hoehme.com/software/tisimBinaries5.0https://www.hoehme.com/images/Software/cellsys_user_guide.pdfUser manual10.1093/bioinformatics/btq43720709692PMC2951083SQANTI3SQANTI3 constitutes the first module of the Functional IsoTranscriptomics (FIT) pipeline, which is an end-to-end strategy to perform isoform-level bioinformatics analyses. The SQANTI3 tool is designed to enable quality control and filtering of long read-defined transcriptomes, which are often rich in artifacts and false-positive isoforms. Therefore, a good curation of the transcriptome is indispensable to proceed with FIT analysis and produce valid, biologically sound conclusions/hypothesis.https://github.com/ConesaLab/SQANTI3sqanti3biotools:sqanti35.5Command-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3512Gene transcriptsLinuxPythonGPL-3.0MatureFree of chargeSpainhttps://github.com/ConesaLab/SQANTI3RepositoryGithub repository for source code access and downloadhttps://github.com/ConesaLab/SQANTI3/releasesDownloads pagehttps://github.com/ConesaLab/SQANTI3/releases/download/v5.5/SQANTI3_v5.5.zipBinariesVersion 5.5 download link from github5.5https://github.com/ConesaLab/SQANTI3/wikiGeneralSQANTI3 main documentation resourcehttps://github.com/ConesaLab/SQANTI3/blob/master/CODE_OF_CONDUCT.mdCode of conducthttps://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-Quality-ControlCommand-line optionsCommand-line options and instructions for the QC submodulehttps://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-filterCommand-line optionsCommand-line options and instructions for the filter submodulehttps://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-rescueCommand-line optionsCommand-line options and instructions for the rescue submodulehttps://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installationInstallation instructionsInstructions to install and use sqanti, either in docker or apptainer containers or in a linux systemhttps://github.com/ConesaLab/SQANTI3/wiki/Tutorial:-running-SQANTI3-on-an-example-datasetQuick start guideBasic tutorial with examples to start using SQANTI3https://github.com/ConesaLab/SQANTI3/releasesRelease notesChangelog and release notes for every versionhttps://github.com/ConesaLab/SQANTI3?tab=readme-ov-file#how-to-cite-sqanti3Citation instructionsCitation instructions are on the end of the Github repository's main pagehttps://github.com/ConesaLab/SQANTI3/wiki/SQANTI3-memory-requeriments-and-paralellizationOtherBenchmarking about the resources needed to run sqanti3 with multiple cores10.1038/s41592-024-02229-2Primary5.1Publication of SQANTI310.1101/gr.222976.117MethodOriginal SQANTI publicationAna Conesaana.conesa@csic.eshttps://orcid.org/0000-0001-9597-311XPablo Atienzapablo.atienza@csic.eshttps://orcid.org/0009-0002-1093-693XPersonMaintainerMaintainer of SQANTI3Fabián Robledofabian.robledo@csic.eshttps://orcid.org/0009-0005-9047-3315PersonMaintainerMaintainer of SQANTI3 and ELIXIR-related contactPIA - Protein Inference AlgorithmsThe main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins.https://github.com/medbioinf/piapiabiotools:pia1.5Command-line toolLibraryDesktop applicationWorkflowhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3120Protein variantsLinuxWindowsMacJavaBSD-3-ClauseKNIMEde.NBIProteomicsBioInfra.ProtCUBiMed.RUBMatureFree of chargeOpen accessProteomicsGermanyhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_0943Mass spectrometry spectrahttp://edamontology.org/format_3713Mascot .dat filehttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3684PRIDE XMLhttp://edamontology.org/format_3711X!Tandem XMLhttp://edamontology.org/format_3702MSFhttp://edamontology.org/format_3681mzTab

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_2206Sequence feature table format (text)http://edamontology.org/format_3765KNIME datatable formathttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3681mzTabhttp://edamontology.org/format_3247mzIdentML

http://edamontology.org/data_0989Protein identifierhttp://edamontology.org/format_2206Sequence feature table format (text)http://edamontology.org/format_3765KNIME datatable formathttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3681mzTabhttp://edamontology.org/format_3247mzIdentML

PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteinshttps://github.com/medbioinf/piaRepositoryhttps://github.com/mpc-bioinformatics/piaSource codehttp://bioconda.github.io/recipes/pia/README.htmlSoftware packagehttps://github.com/mpc-bioinformatics/pia/releasesBinarieshttps://hub.docker.com/r/julianusz/piaContainer filehttps://github.com/medbioinf/pia/wikiGeneralknimeuses10.1021/acs.jproteome.5b0012125938255Primary10.1021/acs.jproteome.8b0072330474983Julian Uszkoreitjulian.uszkoreit@rub.dehttp://orcid.org/0000-0001-7522-4007PersonPrimary contactDeveloperMaintainerCUBiMed.RUBcubimed@rub.deInstituteProviderOpenMSOpen source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView.http://www.openms.deopenmsbiotools:openms2.0.0LibraryWorkbenchhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172MetabolomicsLinuxWindowsMacC++BSD-3-ClauseKNIMEde.NBIProteomicsOpenMSMatureFree of chargehttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_1812Parsinghttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3628Chromatographic alignmenthttp://edamontology.org/operation_3627Mass spectra calibrationhttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3633Retention time predictionhttp://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_3705Isotope-coded protein labelhttp://edamontology.org/operation_3634Label-free quantificationhttp://edamontology.org/operation_3639iTRAQhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3635Labeled quantificationhttp://edamontology.org/operation_3359Splittinghttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/operation_3023Prediction and recognition (protein)http://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_2549OBOhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcMLhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_2549OBOhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcMLhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_2549OBOhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcML

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcML

http://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcML

https://github.com/OpenMS/OpenMSRepositoryhttps://github.com/OpenMS/OpenMSSource codehttp://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/Binarieshttps://github.com/OpenMS/OpenMSSource codehttp://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.htmlGeneral10.1038/nmeth.395927575624Primary10.1007/978-1-60761-987-1_23OtherETH ZürichInstituteProviderEberhard-Karls-Universität TübingenInstituteProviderFreie Universität BerlinInstituteProviderCenter for Integrative Bioinformatics (CiBi)ConsortiumcibiInstituteProviderGeneral Mailinglistopen-ms-general@lists.sourceforge.netSupportGeneral Mailinglistopen-ms-general@lists.sourceforge.netPersonPrimary contactHannes Rösthttp://orcid.org/0000-0003-0990-7488PersonContributorcompareMS2compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.https://github.com/524D/compareMS2comparems2biotools:comparems21.02.0Command-line toolDesktop applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacCJavaScriptMITms-utilsProteomicsMatureFree of chargeProteomicsNetherlandshttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_3272Species treehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_2855Distance matrixhttp://edamontology.org/format_1991megahttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1910newick

https://github.com/524D/compareMS2Repositoryhttps://www.ms-utils.org/compareMS2.htmlSoftware cataloguehttps://research-software-directory.org/software/comparems2Software cataloguehttp://www.ms-utils.org/compareMS2.cSource code1.0http://www.ms-utils.org/compareMS2.htmlBinaries1.0http://www.ms-utils.org/compareMS2.cSource code1.0https://github.com/524D/compareMS2/tree/main/srcSource code2.0https://github.com/524D/compareMS2/tree/mainBinaries2.0http://www.ms-utils.org/compareMS2.htmlGeneralCommand-line optionshttps://github.com/524D/compareMS2GeneralUser manualCommand-line optionsInstallation instructions10.1002/rcm.616222368051Primary1.010.1021/acs.jproteome.2c0045736173614PMC9903320Primary2.010.1021/acs.jproteome.1c0052834523928PMC8491155Review2.0lumc.nlhttps://www.lumc.nlInstituteSupportMagnus Palmbladmagnus.palmblad@gmail.comhttps://github.com/magnuspalmbladhttp://orcid.org/0000-0002-5865-8994PersonDeveloperPrimary contactDocumentorRob Marissenhttps://github.com/524Dhttps://orcid.org/0000-0002-1220-9173PersonDeveloperBiodepot LauncherThe Biodepot Launcher is a desktop application that facilitates installation, management and deployment of containerized bioinformatics workflows. This application provides an interactive and easy-to-use interface to launch containerized analytical workflows that can be used to process biomedical data.https://github.com/BioDepot/biodepot-launcherbiodepot_launcherbiotools:biodepot_launcherDesktop applicationhttp://edamontology.org/topic_0091BioinformaticsLinuxMacWindowsJavaScriptOtherMITFree of chargehttp://edamontology.org/operation_2945Data analysishttps://github.com/BioDepot/biodepot-launcherRepositoryhttps://biodepot.github.io/training/running_bwb/bwb_launcher/OtherTraining portal with screenshots and demo videoshttps://github.com/BioDepot/biodepot-launcherBinarieshttps://github.com/BioDepot/biodepot-launcherInstallation instructionshttps://biodepot.github.io/training/running_bwb/bwb_launcher/Training materialLing-Hong Hunglhhung@uw.eduhttps://orcid.org/0000-0002-5209-2248Primary contactThomas Dahlstromtjdahl@uw.eduhttps://orcid.org/0000-0003-4363-0697DeveloperJohnalbert Garnicajohnnyas@uw.eduhttps://orcid.org/0009-0004-6419-1560DeveloperKa Yee Yeungkayee@uw.eduhttps://orcid.org/0000-0002-1754-7577Primary contactCollagen Mutation Database (CMD)Database of osteogenesis imperfecta and type III collagen variants.https://eds.gene.le.ac.ukcmdbiotools:cmdDatabase portalhttp://edamontology.org/topic_0634PathologyDRCAThttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0957Database metadata

http://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_2331HTML

https://eds.gene.le.ac.uk/docs/LOVD_manual_2.0.pdfRepositoryhttps://eds.gene.le.ac.uk/docs/LOVD_manual_2.0.pdfSource codehttps://eds.gene.le.ac.uk/docs/LOVD_manual_2.0.pdfBinarieshttps://eds.gene.le.ac.uk/docs/index.phpGeneral10.1002/humu.2143821520333PrimaryLeiden University Medical CenterInstituteProviderDRCATProjectDocumentorhttp://www.lovd.nl/2.0/contact.phpPersonPrimary contactCofactoryIdentification of Rossmann folds and prediction of FAD, NAD and NADP specificity.http://cbs.dtu.dk/services/Cofactory/cofactorybiotools:cofactory2.1Web applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual format

identifies Rossmann fold sequence domains and predicts their specificity for the cofactors FAD, NAD or NADPhttp://www.cbs.dtu.dk/services/doc/cofactory-1.0.readmeRepositoryhttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/doc/cofactory-1.0.readmeSource codehttp://www.cbs.dtu.dk/services/doc/cofactory-1.0.readmeBinarieshttp://www.cbs.dtu.dk/services/Cofactory/instructions.phpGeneral10.1002/prot.2453624523134PrimaryCBSInstituteProviderThomas Nordahl Petersentnp@cbs.dtu.dkPersonPrimary contactThe GEM (GEnome Multi-tool) Library (GEM Mapper)A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapperhttps://sourceforge.net/projects/gemlibrary/gemmapperbiotools:gemmapper1Command-line toolhttp://edamontology.org/topic_0077Nucleic acidsLinuxPerlPythonCGPL-3.0http://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_2182FASTQ-like format (text)

http://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAM

Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of accuracy. The Genome Multitool (GEM) mapper can leverage string matching by filtration to search the alignment space more efficiently, simultaneously delivering precision (performing fully tunable exhaustive searches that return all existing matches, including gapped ones) and speed (being several times faster than comparable state-of-the-art tools).https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/Binarieshttp://algorithms.cnag.cat/wiki/The_GEM_libraryGeneral10.1038/nmeth.222123103880PrimaryPaolo RibecaPersonDeveloperSantiago Marco SolaContributorLab Roderic Guigo GroupInstituteProviderLab Roderic Guigo Group: Computational Biology of RNA processing @ Centre for Genomic Regulation Parc de Recerca Biomedica: Dr. Aiguader, 88, 08003 Barcelonacrg.euInstituteProviderPaolo Ribecapaolo.ribeca@pirbright.ac.ukPersonPrimary contactmsaDisplay multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.http://msa.biojs.netmsabiotools:msa1.0.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacJavaScriptApache-2.0Rostlab toolsBioconductorBioJSMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_1711Sequence alignment imagehttp://edamontology.org/format_3547Image format

http://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1270Feature tablehttp://edamontology.org/format_2305GFF

Visualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF NOTE: Actually, all these output types of data should instead be under separate "constant" operations, while the visualisation should be an unary operation, perhaps without an output.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank format

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3508PDF

https://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttp://github.com/wilzbach/msaHelpdeskhttp://www.bioinf.jku.at/software/msa/Mirrorhttps://github.com/wilzbach/msaSource codehttps://cdn.bio.sh/Binarieshttps://github.com/wilzbach/msa/blob/master/LICENSETerms of usehttp://msa.biojs.netGeneral10.1093/bioinformatics/btw47427412096PMC5181560Primary10.1093/bioinformatics/btv49426315911OtherSebastian WilzbachPersonDeveloperIan SillitoeContributorGuy YachdavContributorBenedikt RauscherContributorTatyana GoldbergContributorTechnische Universität MünchenInstituteProviderGoogle Summer of Code (GSoC) 2014Funding agencyContributorBioJSInstituteProviderhttp://github.com/wilzbach/msaPersonPrimary contactUlrich Bodenhoferbodenhofer@bioinf.jku.atPersonPrimary contactAquariaSimplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...).http://aquaria.wsaquariabiotools:aquaria1Web APIWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMacJavaScriptJavaGPL-2.0Odonoghuelab toolsRostlab toolsMatureFree of chargehttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_1063Sequence identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1869Organism identifierhttp://edamontology.org/format_2330Textual formatYou can find sequences based on a keyword search. For the identified sequence, Aquaria retrieves sequence-to-structure alignments from the PSSH2 database and visualises those on the web page. At the same time, a selected alignment is visualised in the 3D viewer (by default the one with most identical residues between sequence and structure). accession number, ID or part of the name or alias from UniProt Organism names used in UniProt; Homo sapiens used by defaulthttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_1096Sequence accession (protein)http://edamontology.org/format_1963UniProtKB format

http://edamontology.org/data_0893Sequence-structure alignmenthttp://edamontology.org/format_3464JSON

web service to get matching structures with alignment data for a given protein sequence Uniprot accession of query protein glued into the query URL: aquaria.ws/<UniprotAcc>.json json representation of one or more sequence-to-structure alignments annotated with alignment statisticshttps://github.com/ODonoghueLab/AquariaRepositoryhttp://aquaria.ws/help/Aquaria3D_QR_v1.pdfSource codehttp://aquaria.ws/help/Aquaria3D_QR_v1.pdfBinarieshttps://www.youtube.com/watch?v=FAQ3yVGYSzY&feature=youtu.beGeneral10.1038/nmeth.325825633501PrimaryChristian StoltePersonDeveloperKenneth S SabirPersonDeveloperSeán I O'DonoghuePersonDeveloperAndrea SchafferhansPersonDeveloperNelson PerdigãoContributorBurkhard RostContributorVivian HoContributorManfred RoosContributorBenjamin WellmannContributorJulian HeinrichContributorMaria KalemanovContributorFabian A BuskeContributorDepartment for Bioinformatics and Computational Biology, Technische Universität MünchenInstituteProviderDivision of Genomics and Epigenetics, Garvan Institute of Medical Research, SydneyInstituteProviderDigital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), SydneyInstituteProviderSchool of Molecular Bioscience, The University of SydneyInstituteProviderAmazon AWSConsortiumCSIRO's OCE Science Leader program and its Computational and Simulation Sciences platformFunding agencyContributorAlexander von Humboldt FoundationFunding agencyContributorRostLabInstituteProviderSeán I. O'Donoghuesean@odonoghuelab.orgSupportAndrea Schafferhansandrea.schafferhans@rostlab.orgSupportSeán O'Donoghuesean@odonoghuelab.orgPersonPrimary contactAndrea Schafferhansandrea.schafferhans@rostlab.orgPersonPrimary contactLocTree3Prediction of protein subcellular localization in 18 classes for eukaryota, 6 for bacteria and 3 for archaea.https://rostlab.org/services/loctree3/loctree3biotools:loctree31.0.8Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_2229Cell biologyLinuxPHPJavaPerlJavaScriptGPL-3.0Rostlab toolsPredictProteinMatureFree of chargehttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSV

Prediction of protein sucellular localization in 18 classes for eukaryota, 6 classes for bacteria and 3 for archaea using homology searches (PSI-BLAST) and machine learning (SVM) User can provide one or more sequences in FASTA format The prediction output contains: prediction score, from 1 (weak prediction) to 100 (strong prediction); one of 18 localization classes for eukaryota, 6 for bacteria and 3 for archaea; GO identifier; GO term; prediction source (PSI-BLAST or SVM)https://rostlab.org/owiki/index.php/PackagesRepositoryhttps://rostlab.org/owiki/index.php/PackagesSource codehttps://rostlab.org/owiki/index.php/PackagesBinarieshttps://rostlab.org/owiki/index.php/Loctree3General10.1093/nar/gku39624848019PMC4086075Primary10.1093/bioinformatics/bts39022962467PMC3436817OtherMaximilian HechtPersonDeveloperGuy YachdavPersonDeveloperTimothy KarlPersonDeveloperTobias HampPersonDeveloperTatyana GoldbergPersonDeveloperBurkhard RostContributorHenrik NielsenContributorTechnische Universität MünchenInstituteProviderAlexander von Humboldt Foundation through German Federal Ministry for Education and ResearchFunding agencyContributorErnst Ludwig Ehrlich StudienwerkFunding agencyContributorRostLabInstituteProviderlocalization@rostlab.orghttps://rostlab.org/services/loctree3/PersonPrimary contactThe Flux SimulatorModel RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.http://sammeth.net/confluence/display/SIM/Homethe_flux_simulatorbiotools:the_flux_simulator1.2.1Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxMacJavaBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_3566Simulated gene expression data generationhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2306GTFhttp://edamontology.org/data_0006DataThe Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. Our models do not simulate molecular processes on the level of atoms, but represent a collection of deterministic approaches with a minimal set of parameters that can be estimated from observations of the experiment that is to be reproduced. Model development has to be understood as an iterative process to a maximal convergence of "model world" and "real world". It always requires a careful evaluation of all hypotheses and assumptions by comparison with experimental data.http://sammeth.net/bitbucket/projects/BARNA/repos/barna/browse/barna.simulatorRepositoryhttp://sammeth.net/confluence/display/SIM/2+-+DownloadSource codehttp://sammeth.net/confluence/display/SIM/2+-+DownloadBinarieshttp://sammeth.net/confluence/display/SIM/HomeGeneral10.1093/nar/gks66622962361PMC3488205PrimaryMicha SammethPersonDeveloperLab Roderic Guigo GroupInstituteProvidercrg.euInstituteProviderMicha Sammethmicha@sammeth.netPersonPrimary contactAStalavistaAlternative splicing trascriptional landscape visualization tool retrieves all alternative splicing events from generic transcript annotations.http://sammeth.net/confluence/display/ASTA/Homeastalavistabiotools:astalavista3.2Command-line toolhttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxWindowsMacJavaBSD-3-ClauseFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/data_1276Nucleic acid features

http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_3547Image format

The AStalavista web server extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, AStalavista detects the variations in their splicing structure and identify all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. AStalavista provides a vizual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase,...http://sammeth.net/bitbucket/scm/barna/barna.gitRepositoryhttp://artifactory.sammeth.net/artifactory/barna/barna/barna.astalavista/3.2/astalavista-3.2.tgzSource codehttp://sammeth.net/confluence/display/ASTA/2+-+DownloadBinarieshttp://sammeth.net/confluence/display/ASTA/2+-+DownloadGeneral10.1101/gr.121947.11122113879PMC3290788PrimaryMicha SammethPersonDeveloperLab Roderic Guigo GroupInstituteProvidercrg.euInstituteProviderMicha Sammethmicha@sammeth.netPersonPrimary contactSelenoprofiles3Pipeline for profile-based protein finding in genomes.http://big.crg.cat/services/selenoprofilesselenoprofiles3biotools:selenoprofiles33.0Command-line toolhttp://edamontology.org/topic_0160Sequence sites, features and motifsGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_3494DNA sequence

http://edamontology.org/data_1276Nucleic acid features

Provided one or more protein alignments, it scans a target genome (or any other nucleotide database) and reports the gene structures of homologous genes. It can be used to easily characterize any protein family of interest across a massive amount of sequenced genomes, allowing a finely tuned filtering of results. Or it can be used with comprehensive sets of input profiles, in order to completely annotate by homology one or more genomes.https://github.com/marco-mariotti/selenoprofilesRepositoryhttp://genome.crg.es/~mmariotti/selenoprofiles_3_installation.tarSource codehttp://genome.crg.es/~mmariotti/selenoprofiles_manual.pdfBinarieshttp://big.crg.cat/services/selenoprofilesGeneral10.1093/bioinformatics/btq51620861026PMC2958745PrimaryMarco MariottiPersonDeveloperDidac SantesmassesContributorLab Roderic Guigo GroupInstituteProvidercrg.euInstituteProviderDidac Santesmasses & Marco Mariottididac.santesmasses@crg.euPersonPrimary contactMotifLabGeneral workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. It can improve performance of binding site predictions by allowing users to integrate several motif discovery tools, as well as different types of data: phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression.http://www.motiflab.orgmotiflabbiotools:motiflab1.8Command-line toolDesktop applicationWorkbenchhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_0749Transcription factors and regulatory sitesLinuxWindowsMacJavaNeLSELIXIR-NorwaySEQwikiNTNU toolsMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://www.motiflab.org/index.php?page=downloadRepositoryhttp://www.motiflab.org/index.php?page=contactHelpdeskhttp://www.motiflab.org/MotifLab_source.zipSource codehttp://www.motiflab.org/index.php?page=downloadBinarieshttp://www.motiflab.org/index.php?page=publicationsCitation instructionshttp://www.motiflab.org/index.php?page=documentationGeneral10.1186/1471-2105-14-923323883PMC3556059Primary10.1093/bioinformatics/btq35720628076PMC2922893OtherKjetil KlepperPersonDeveloperFinn DrabløsContributorELIXIR-NorwayConsortiumNeLS (Norwegian e-Infrastructure for Life Sciences)ConsortiumThe National Programme for Research in Functional Genomics in NorwayFunding agencyContributorNorwegian infrastructure for bioinformatics ELIXIR.noFunding agencyContributorNTNUInstituteProviderKjetil Klepperkjetil.klepper@ntnu.nohttp://www.motiflab.org/index.php?page=contactMaintainerFinn Drabløsfinn.drablos@ntnu.nohttp://www.motiflab.org/index.php?page=contactSupportKjetil Klepperkjetil.klepper@ntnu.nohttp://www.motiflab.org/index.php?page=contactPersonPrimary contactFinn Drabløsfinn.drablos@ntnu.nohttp://www.motiflab.org/index.php?page=contactPersonPrimary contactApache TavernaOpen source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.http://taverna.incubator.apache.org/apache_tavernabiotools:apache_taverna3Web APIWorkbenchCommand-line toolWeb serviceWeb applicationDesktop applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0202Pharmacologyhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_3473Data miningLinuxWindowsMacJavaRubyApache-2.0MatureFree of chargehttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0224Query and retrievalhttps://github.com/apache/?query=tavernaRepositoryhttp://taverna.incubator.apache.org/community/listsHelpdeskhttp://taverna.incubator.apache.org/download/code/Source codehttp://taverna.incubator.apache.org/download/Binarieshttp://taverna.incubator.apache.org/community/citeCitation instructionshttp://taverna.incubator.apache.org/documentation/General10.1093/nar/gkt32823640334PMC3692062PrimaryApache Software FoundationInstituteProvidercs.manchester.ac.ukInstituteProviderApache Taverna communityhttp://taverna.incubator.apache.org/communityDeveloperApache Taverna communityhttp://taverna.incubator.apache.org/communityPersonPrimary contactApache Taverna mailing listshttp://taverna.incubator.apache.org/community/listsPersonPrimary contactGenomeRNAiThis database makes available RNAi phenotype data extracted from the literature, or submitted by data producers directly, for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity.http://www.genomernai.org/genomernaibiotools:genomernaiDatabase portalhttp://edamontology.org/topic_3523RNAi experimentLinuxWindowsMacde.NBIhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/data_1089FlyBase IDhttp://edamontology.org/data_1033Ensembl gene IDhttp://edamontology.org/data_1026Gene symbolhttp://edamontology.org/data_1187PubMed IDhttp://edamontology.org/data_2118Person identifierhttp://edamontology.org/data_3275Phenotype namehttp://edamontology.org/data_0842Identifierhttp://edamontology.org/data_1027Gene ID (NCBI)

http://edamontology.org/data_2080Database search results

http://edamontology.org/data_2884Plot

Last name of first author RNAi reagent identifierhttp://www.genomernai.org/DownloadAllExperimentsFormRepositoryhttp://www.genomernai.org/DownloadAllExperimentsFormSource codehttp://www.genomernai.org/DownloadAllExperimentsFormBinarieshttp://www.genomernai.org/About#Citation instructionshttp://rnai-screening-wiki.dkfz.de/confluence/display/genomernai/HomeGeneral10.1093/nar/gks117023193271PMC3531141PrimaryEsther SchmidtPersonDeveloperBenedikt RauscherPersonDeveloperOliver PelzPersonDeveloperMichael BoutrosPersonDeveloperGerman Cancer Research CenterInstituteProviderhdhubInstituteProvidercontact@genomernai.orgPersonPrimary contactSWIFTProgram for fast local alignment search, guaranteeing to find epsilon-matches between two sequences. An epsilon-match is a local alignment above a given length with an error rate of at most epsilon.https://bibiserv.cebitec.uni-bielefeld.de/swiftswiftbiotools:swift1Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxMacBiGide.NBIMatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttps://bibiserv.cebitec.uni-bielefeld.de/swift?id=swift_view_downloadRepositoryhttp://bibiserv.cebitec.uni-bielefeld.de/resources/download/swift/swift-1.0.1-src.tar.gzSource codehttps://bibiserv.cebitec.uni-bielefeld.de/swift?id=swift_view_downloadBinarieshttps://bibiserv.cebitec.uni-bielefeld.de/swiftGeneral10.1089/cmb.2006.13.29616597241PrimaryKim R. RasmussenPersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactPoSSuMsearch2Significant speedup of database searches with HMMs by search space reduction with PSSM family models.https://bibiserv.cebitec.uni-bielefeld.de/possumsearch2possumsearch2biotools:possumsearch22Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxMacBiGide.NBIMatureFree of charge (with restrictions)http://edamontology.org/operation_2403Sequence analysishttps://bibiserv.cebitec.uni-bielefeld.de/possumsearch2?id=possumsearch_downloadRepositoryhttps://bibiserv.cebitec.uni-bielefeld.de/possumsearch2?id=possumsearch_downloadSource codehttp://bibiserv.cebitec.uni-bielefeld.de/resources/download/possumsearchBinarieshttps://bibiserv.cebitec.uni-bielefeld.de/possumsearch2General10.1093/bioinformatics/btp59319828575PMC2788931PrimaryRobert HomannPersonDeveloperMichael BeckstettePersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactPoSSuMsearchThis tool find matches of PSSM in large databases. Our approach preprocesses the search space and builds an enhanced suffix array which is stored on file. Since ESAsearch benefits from small alphabets, we present a variant operating on sequences recoded according to a reduced alphabet. We also address the problem of non-comparable PSSM-scores by developing a method which allows to efficiently compute a matrix similarity threshold for a PSSM, given an E-value or a P-value.https://bibiserv.cebitec.uni-bielefeld.de/possumsearchpossumsearchbiotools:possumsearch1Libraryhttp://edamontology.org/topic_0080Sequence analysisLinuxCBiGide.NBIMatureFree of charge (with restrictions)http://edamontology.org/operation_2403Sequence analysishttps://bibiserv.cebitec.uni-bielefeld.de/possumsearch?id=possumsearch_downloadRepositoryhttps://bibiserv.cebitec.uni-bielefeld.de/possumsearch?id=possumsearch_downloadSource codehttps://bibiserv.cebitec.uni-bielefeld.de/resources/download/possumsearch/Binarieshttps://bibiserv.cebitec.uni-bielefeld.de/possumsearchGeneral10.1186/1471-2105-7-38916930469PMC1635428PrimaryRobert HomannPersonDeveloperMichael BeckstettePersonDeveloperCeBiTecInstituteProviderBielefeld universityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactJAliAlignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.http://bibiserv.cebitec.uni-bielefeld.de/jalijalibiotools:jali1.3Web APIWeb applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCBiGide.NBIMatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3154Protein alignmenthttp://edamontology.org/format_1929FASTAComputes Jumping ALIgnments from a protein sequence and an alignment of a protein family.http://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_downloadRepositoryhttp://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_downloadSource codehttp://bibiserv.cebitec.uni-bielefeld.de/resources/download/jaliBinarieshttp://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_manualGeneral10.1089/10665270276103417212487762PrimaryJens StoyePersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactGUUGleRNA secondary structure analysis often requires searching for potential helices in large sequence data. We present a utility program that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.http://bibiserv.cebitec.uni-bielefeld.de/guugleguuglebiotools:guugle1.2Web APIWeb applicationCommand-line toolhttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacCBiGide.NBIMatureFree of chargehttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2975Nucleic acid sequence (raw)http://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1925codatahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1211unambiguous pure nucleotidehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_1216unambiguous pure rna sequencehttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1942ig

http://edamontology.org/data_2955Sequence report

We present a utility program that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs.https://bibiserv.cebitec.uni-bielefeld.de/guugle?id=guugle_view_downloadRepositoryhttps://bibiserv.cebitec.uni-bielefeld.de/applications/guugle/resources/downloads/guugle-1.2.src.tar.gzSource codehttps://bibiserv.cebitec.uni-bielefeld.de/guugle?id=guugle_view_downloadBinarieshttps://bibiserv.cebitec.uni-bielefeld.de/guugle?id=guugle_manualGeneral10.1093/bioinformatics/btk04116403789PrimaryWolfgang GerlachPersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactAggloIndelThis tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. It does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity or polyploidy. Taking paired ends mapped to a reference genome as input, it merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account.http://bibiserv.cebitec.uni-bielefeld.de/agglodelaggloindelbiotools:aggloindel1Command-line toolhttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacJavaBiGide.NBIMatureFree of chargehttp://edamontology.org/operation_3202Polymorphism detectionhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/data_1288Genome maphttp://edamontology.org/format_2572BAM

http://edamontology.org/data_1276Nucleic acid features

Taking paired ends mapped to a reference genome as input, it iteratively merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into accounthttps://bibiserv.cebitec.uni-bielefeld.de/agglodel?id=agglodel_downloadRepositoryhttps://bibiserv.cebitec.uni-bielefeld.de/applications/agglodel/resources/downloads/aggloIndel.jarSource codehttps://bibiserv.cebitec.uni-bielefeld.de/applications/agglodel/resources/downloads/aggloIndel.jarBinarieshttps://bibiserv.cebitec.uni-bielefeld.de/agglodelGeneral10.1186/1471-2164-14-s1-s1223369161PMC3549816Maureen SmithPersonDeveloperRoland WittlerPersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactCG-CATWith current sequencing technologies, it is feasible to generate a lot of reads for a given genome. However, the assembly usually ends up in a set of contigs with gaps between them. If the sequences of one (or several) related genome(s) are already known, this information can be used to estimate the order and orientation of the contigs towards each other. This helps in the finishing phase of a sequencing project since it eases the design of specific primer sequences to fill the gaps.http://bibiserv.cebitec.uni-bielefeld.de/cgcatcg-catbiotools:cg-cat1Desktop applicationhttp://edamontology.org/topic_0196Sequence assemblyLinuxWindowsMacJavaGPL-2.0BiGide.NBIMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/operation_0490Dot plot plottinghttp://edamontology.org/data_2975Nucleic acid sequence (raw)http://edamontology.org/format_1954Pearson format

http://edamontology.org/data_0862Dotplot

http://edamontology.org/data_3181Sequence assembly report

Match a set of contigs to a related reference genome to order and orient the contigs based on that reference. The mapping is visualized in an interactive synteny plot.http://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/data_2975Nucleic acid sequence (raw)http://edamontology.org/format_1954Pearson formathttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick

http://edamontology.org/data_3181Sequence assembly report

The program treecat can be used to estimate an ordering for a set of contigs. A so called layout graph shows the unique order where possible and gives alternatives where necessary. The layout graph is calculated based on the matches to several related genomes as well as the information given by a phylogenetic tree of the involved species.http://bibiserv.cebitec.uni-bielefeld.de/cgcat?id=cgcat_downloadRepositoryhttp://bibiserv.cebitec.uni-bielefeld.de/cgcat?id=cgcat_downloadSource codehttp://bibiserv.cebitec.uni-bielefeld.de/cgcat?id=cgcat_downloadBinarieshttp://bibiserv.cebitec.uni-bielefeld.de/cgcat?id=cgcat_manualGeneral10.1186/1748-7188-5-320047659PMC2826331Primary10.1093/bioinformatics/btp69020015948PMC2820676OtherPeter HusemannPersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibiadm@cebitec.uni-bielefeld.dePersonPrimary contactRNAhybridTool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.http://bibiserv.cebitec.uni-bielefeld.de/rnahybridrnahybridbiotools:rnahybrid2.2.1Web APIWeb applicationCommand-line toolhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0349Sequence database search (by property)http://edamontology.org/operation_0415Nucleic acid feature detectionhttp://edamontology.org/operation_0475Nucleic acid structure predictionhttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_2975Nucleic acid sequence (raw)http://edamontology.org/format_1925codatahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_1210pure nucleotidehttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1942ighttp://edamontology.org/data_2975Nucleic acid sequence (raw)http://edamontology.org/format_1925codatahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_1210pure nucleotidehttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1942ig

http://edamontology.org/data_1584Nucleic acid enthalpy

http://edamontology.org/data_0880RNA secondary structure

http://edamontology.org/data_1584Nucleic acid enthalpy

http://edamontology.org/data_3128Nucleic acid structure report

http://edamontology.org/data_1276Nucleic acid features

calculates a minimal free energy hybridization of RNA sequence(s) and miRNA(s)http://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_downloadRepositoryhttp://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_downloadSource codehttp://bibiserv.cebitec.uni-bielefeld.de/resources/download/rnahybridBinarieshttp://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_manual_manualGeneral10.1261/rna.524860415383676PMC1370637PrimaryMarc RehmsmeierPersonDeveloperBielefeld universityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactSNAP2Method that predicts the effects of single amino acid substitutions in a protein on the protein's function using neural networks.https://github.com/Rostlab/SNAP2snap2biotools:snap21Command-line toolWeb applicationhttp://edamontology.org/topic_2885DNA polymorphismLinuxMachttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1772Scorehttp://edamontology.org/format_2330Textual format

Prediction of SNP influence on protein function between neutral and effect. "functional effect"-score between -100 (neutral) and 100 (effect) for every possible SNP at every position of the input sequencehttps://github.com/Rostlab/SNAP2Repositoryhttps://github.com/Rostlab/SNAP2Source codehttps://github.com/Rostlab/SNAP2Binarieshttps://github.com/Rostlab/SNAP2Citation instructionsGeneral10.1186/1471-2164-16-s8-s126110438PMC4480835Maximilian HechtPersonDevelopermytum.deInstituteProviderRostlabassistant@rostlab.orghttps://rostlab.orgPersonPrimary contactLivermore Metagenomics Analysis ToolkitEfficiently assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick 'single pass' analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. Its approach is kmer-based.http://computation.llnl.gov/projects/livermore-metagenomics-analysis-toolkitlivermore_metagenomics_analysis_toolkitbiotools:livermore_metagenomics_analysis_toolkitVersion 1-2-6Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxMacMatureFree of chargehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2546FASTA-like

http://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_2330Textual format

Using a custom precomputed reference database with a fast searchable index to classify short reads against genomes of viruses, bacteria, archaea, protozoa, fungi, and several variants of the human genome. Submission sequence is a fasta (or fastq) formatted sequence Outputs are 5 tab-separated summary text files, 1 log file and a number of individual output files.https://sourceforge.net/projects/lmat/Repositoryhttps://sourceforge.net/projects/lmat/Source codehttps://sourceforge.net/projects/lmat/Binarieshttp://computation.llnl.gov/projects/livermore-metagenomics-analysis-toolkitGeneral10.1007/s10586-013-0309-0Other10.1093/bioinformatics/btt38923828782PMC3753567Otherebi.ac.ukInstituteProviderMaya B Gokhalemaya@llnl.govPersonPrimary contactMETA-GECKOSet of post-processing tools aimed at improving the taxonomical classification and at providing additional information to enhance metagenomics analyses. The developed tools provide additional proofs in the presence of low-abundant species, information of the mapping quality in coding and noncoding regions, etc.http://bitlab-es.com/gecko/template.php#META-GECKOmeta-geckobiotools:meta-gecko1Command-line toolWeb applicationhttp://edamontology.org/topic_3174MetagenomicsLinuxWindowsMacCGPL-3.0ELIXIR-ESEmergingFree of chargehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTA

http://edamontology.org/data_1872Taxonomic classificationhttp://edamontology.org/format_2333Binary format

Taxonomic classification and species abundance analysis of metagenomic samples Metagenomic sample Genome database Taxonomic classificationhttp://bitlab-es.com/gecko/documents/METAGECKO-GuidedExercise.pdfRepositoryhttp://bitlab-es.com/gecko/documents/METAGECKO-GuidedExercise.pdfSource codehttp://bitlab-es.com/gecko/files/METAGECKO-bin-x64.tar.gzBinarieshttp://bitlab-es.com/gecko/template.php#META-GECKOGeneral10.1186/s12864-016-3063-x27801291PMC5088524Primaryuma.esInstituteProviderEsteban Pérez-Wohlfeilestebanpw@uma.esPersonPrimary contact