nalloNallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences.https://github.com/genomic-medicine-sweden/nallonallobiotools:nallo0.12.0http://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3295EpigeneticsGroovyJavaMITFree of chargehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2545FASTQ-like format

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3327BAI

https://github.com/genomic-medicine-sweden/nalloRepositoryhttps://genomic-medicine-sweden.github.io/nallo/latest/User manual10.1093/BIOINFORMATICS/BTAG08641712762PMC12988770Lars Feuklars.feuk@igp.uu.sehttps://orcid.org/0000-0003-2355-2919PersonProteinsPlusThe ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.https://proteins.plusproteinsplusbiotools:proteinsplusWeb serviceWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://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_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_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDF

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

prediction of protonation states and tautomers and placement of hydrogen atomshttp://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 complexeshttp://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_1476PDBhttp://edamontology.org/format_3814SDFhttp://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 channelshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://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_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 crystallographyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1772Score

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

protein-protein interface classification (permanent, transient, crystal artifact)http://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://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_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1197InChIhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3816Mol2http://edamontology.org/format_3814SDFhttp://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_1476PDBhttp://edamontology.org/format_3814SDF

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 moleculeshttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://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_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 detectionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://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_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_1772Score

http://edamontology.org/data_2019Map data

small molecule binding site detection and druggability assessmenthttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://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_1566Protein-ligand interaction reporthttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3464JSON

http://edamontology.org/data_2992Protein structure imagehttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3464JSON

http://edamontology.org/data_1712Chemical structure imagehttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3464JSON

http://edamontology.org/data_0906Protein interaction datahttp://edamontology.org/format_2330Textual format

2D interaction diagram drawing and editinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://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_0906Protein interaction datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1772Score

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

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

metal complex geometry predictionhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://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_1566Protein-ligand interaction reporthttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_1712Chemical structure imagehttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_2992Protein structure imagehttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3603PNG

2D interaction diagram drawinghttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://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_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 analysishttp://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 generationhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0306Text mininghttp://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_2080Database search resultshttp://edamontology.org/format_2330Textual format

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_1497Root-mean-square deviation

textual, numerical, and chemical 3D searches in the PDBhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://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_1460Protein structurehttp://edamontology.org/format_1476PDB

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

water molecule placementhttps://proteins.plusServicehttps://proteins.plus/help/indexGeneraldogsitescorerincludesdogsite3includesediaincludessienaincludesmetalizerincludesstructureprofilerincludesjamdaincludesgeomineincludesmicrominerincludesposeeditincludesposeviewincludesprotossincludeslifesoaksincludesppiincludes10.1093/nar/gkx33328472372PMC5570178Primary10.1093/nar/gkaa23532297936PMC7319454Usage10.1093/nar/gkac30535489057PMC9252762Usage10.1093/nar/gkaf37740326518PMC12230695UsageProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderSIENASIENA 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 Bioinformatics00g30e956InstituteProviderSPALNGenome mapping and spliced alignment of cDNA or amino acid sequenceshttps://github.com/ogotoh/spalnspalnbiotools:spalnver.3.0.8bCommand-line toolhttp://edamontology.org/topic_0102MappingCPerlC++GPL-2.0Maturehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1234Sequence set (nucleic acid)

http://edamontology.org/data_0863Sequence alignment

https://github.com/ogotoh/spalnRepositoryhttps://github.com/ogotoh/spalnGeneral10.1093/nar/gkag35742134803PMC1317563310.1093/bioinformatics/btn4601872804310.1093/nar/gks70822848105PMC348821110.1093/bioinformatics/16.3.1901086901210.1093/bioinformatics/btae51739152995PMC1136180910.1007/978-1-0716-1036-7_53328988710.1093/bioinformatics/btl06716500940Osamu Gotohgotoh.osamu.67a@st.kyoto-u.ac.jphttps://orcid.org/0009-0002-6750-1945PersonVerityMapVerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.https://github.com/ablab/VerityMapVerityMapbiotools:VerityMaphttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622GenomicsCCUDAPythonC++GPL-3.0Maturehttp://edamontology.org/operation_0523Mapping assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3003BED

https://github.com/ablab/tandemQUAST/issuesIssue tracker10.1093/bioinformatics/btaa44032657355PMC7355294SNP-sitesFinds SNP sites from a multi-FASTA alignment file.https://sanger-pathogens.github.io/snp-sites/snp-sitesbiotools:snp-sites2.5.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_2885DNA polymorphismLinuxCGPL-3.0Open accesshttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCF

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

snp-sites my_alignment.aln snp-sites my_gzipped_alignment.aln.gzhttps://github.com/sanger-pathogens/snp-sitesRepositoryhttps://sanger-pathogens.github.io/snp-sites/General10.1099/mgen.0.00005628348851PMC5320690Primarysam2intervalA Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalsam2intervalbiotools:sam2intervalScripthttp://edamontology.org/topic_0622GenomicsMacWindowsLinuxPythonMITEmergingFree of chargeOpen accessGalaxyhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAM

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2572BAM

https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalRepositoryRepeatAfterMeRepeatAfterMe is a package for the extension of repetitive DNA cores. The tool automatically extends a multiple sequence alignment that may represent only a fragment of a longer repetitive sequence family.https://github.com/Dfam-consortium/RepeatAfterMerepeataftermebiotools:repeataftermev0.0.7Command-line toolhttp://edamontology.org/topic_0622GenomicsMacLinuxCCC0-1.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_30092bithttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/format_3585bed6

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTA

./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bitRobert HubleyPersonDeveloperslow5-doradoFork of dorado (high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads) that support S/BLOW5https://github.com/hiruna72/slow5-doradoslow5-doradobiotools:slow5-dorado1.1.1Command-line toolhttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_0080Sequence analysisLinuxC++Otherhttp://edamontology.org/operation_3185Base-callinghttp://edamontology.org/data_0924Sequence trace

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2572BAM

bwa-methbwa-meth is a tool for alignment of Bisulfite sequencing reads.https://github.com/brentp/bwa-methbwa-methbiotools:bwa-meth0.2.9Command-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622GenomicsLinuxPythonMITMatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2573SAM

10.48550/arXiv.1401.1129PreprintPLASTPLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a "seed-and-extend approach" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.https://github.com/tischulz1/plastpangenome-blastbiotools:pangenome-blast0.0.1-0.2.0Command-line toolhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0080Sequence analysisLinuxMacWindowsC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1211unambiguous pure nucleotidehttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_3975GFA 1http://edamontology.org/format_2333Binary format

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

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

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

If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fastahttps://gitlab.ub.uni-bielefeld.de/gi/plastRepositoryhttps://github.com/tischulz1/plastMirrorhttps://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.mdGeneral10.1093/bioinformatics/btab07733532821PMC8388040PrimaryMethodBenchmarking studyBielefeld Universityhttps://www.uni-bielefeld.de/InstituteProviderGenome Informaticshttps://gi.cebitec.uni-bielefeld.de/InstituteProviderTizian Schulzplast-service@cebitec.uni-bielefeld.dehttps://orcid.org/0000-0003-0744-7078PersonDeveloperBioMaS (Bioinformatic analysis of Metagenomic amplicons)BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills.http://itsonewb.cloud.ba.infn.it/galaxy/tool_runner?tool_id=biomas2_wrapperbiomas_bioinformatic_analysis_of_metagenomic_ampliconsbiotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons1.0Web applicationhttp://edamontology.org/topic_3391OmicsLinuxMacWindowsBashPythonNot licensedEmergingFree of charge (with restrictions)Open access (with restrictions)ToolsMarine MetagenomicsItalyhttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2573SAM

http://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1910newick

http://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2573SAM

10.1186/s12859-015-0595-z26130132PMC4486701MethodBruno Fossob.fosso@ibiom.cnr.ithttps://orcid.org/0000-0003-2324-086XPersonDeveloperResearcher at CNR-IBIOMGraziano Pesolegraziano.pesole@uniba.ithttps://orcid.org/0000-0003-3663-0859PersonPrimary contactFull Professor of Molecular Biology at University of BariMonica Santamariam.santamaria@ibiom.cnr.ithttps://orcid.org/0000-0003-1488-6052PersonContributorResearcher at CNR-IBIOMD-GENIESD-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.https://dgenies.toulouse.inrae.fr/d-geniesbiotools:d-geniesWeb applicationCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysisMacLinuxPythonShellGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3182Genome alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/data_3494DNA sequence

http://edamontology.org/data_1383Nucleic acid sequence alignment

http://edamontology.org/data_2161Sequence similarity plot

http://edamontology.org/operation_0490Dot plot plottinghttp://edamontology.org/data_1383Nucleic acid sequence alignment

http://edamontology.org/data_2161Sequence similarity plot

https://github.com/genotoul-bioinfo/dgeniesRepositoryhttps://dgenies.readthedocs.io/en/latest/index.htmlGeneral10.7717/peerj.495829888139PMC5991294PrimaryFloréal CabanettesPersonDeveloperChristophe Kloppchristophe.klopp@inrae.frhttps://orcid.org/0000-0001-7126-5477PersonPrimary contactPhilippe Bordronhttps://orcid.org/0000-0003-1975-0920PersonPrimary contactDeveloperVincent DominguezDeveloperGenoToul bioinformatics facilityhttp://bioinfo.genotoul.fr/DivisionProviderJalviewJalview 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/0000-0002-9014-5355SILVA rRNA databaseSILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).https://www.arb-silva.desilvabiotools:silvaRRID:SCR_006423rridWeb applicationDatabase portalhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0632Probes and primersCC-BY-4.0de.NBIde.NBI-biodataDSMZ Digital DiversityMatureFree of chargeOpen accessDataGermanyhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1868Taxonhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1046Strain namehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1088Article IDhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_2909Organism namehttp://edamontology.org/format_1964plain text format (unformatted)

http://edamontology.org/data_2955Sequence reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_3830ARBhttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_3830ARBhttp://edamontology.org/format_1984FASTA-aln

The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.http://edamontology.org/operation_2419Primer and probe designhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1207nucleotidehttp://edamontology.org/data_1240PCR primershttp://edamontology.org/format_1207nucleotide

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2331HTML

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

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3830ARBhttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_3830ARBhttp://edamontology.org/format_1984FASTA-aln

The SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets. TestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_0547Phylogenetic inference (maximum likelihood and Bayesian methods)http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3830ARBhttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick

http://edamontology.org/data_1872Taxonomic classificationhttp://edamontology.org/format_3752CSV

The Alignment, Classification and Tree Service (ACT) of SILVA allows to align and optionally classify sequences using the SILVA Incremental Aligner (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred using FastTree or RAxML.https://www.arb-silva.de/browser/ServiceSILVA Taxonomy Browserhttps://www.arb-silva.de/search/ServiceSILVA metadata searchhttps://www.arb-silva.de/aligner/ServiceACT: Alignment, Classification and Tree Servicehttps://www.arb-silva.de/search/testprobe/ServiceSILVA Probe Match and Evaluation Toolhttps://www.arb-silva.de/search/testprime/ServiceSILVA Primer Evaluation Toolhttps://treeviewer.arb-silva.de/ServiceWeb-based viewer for the SILVA guide treeshttps://www.arb-silva.de/download/archive/Downloads pageSILVA dataset archivehttps://www.arb-silva.de/silva-license-information/Terms of usehttps://www.arb-silva.de/contact/Citation instructionshttps://www.arb-silva.de/documentation/Generalhttps://www.arb-silva.de/documentation/faqs/FAQsilvangsusedByd3hubincludedIn10.1093/nar/gks121923193283PMC3531112Primary10.1093/nar/gkt120924293649PMC3965112Other10.1093/nar/gkm86417947321PMC2175337Other10.1093/bioinformatics/bts25222556368PMC3389763Other10.1016/j.jbiotec.2017.06.119828648396Review10.1186/s12859-017-1841-3OtherLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshub@dsmz.dehttps://www.dsmz.degrid.420081.f02tyer376InstituteProviderSILVA Teamcontact@arb-silva.dehttps://www.arb-silva.de/contact/team/grid.507782.f027z9pz32DivisionPrimary contactZoonomiaThe Zoonomia Project provides access to genomic data including assemblies, annotations and alignments for 240 mammalian species.https://zoonomiaproject.org/zoonomiaprojectbiotools:zoonomiaprojectDatabase portalhttp://edamontology.org/topic_3050BiodiversityMatureFree of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_2909Organism namehttp://edamontology.org/data_1045Species name

http://edamontology.org/data_1383Nucleic acid sequence alignment

http://edamontology.org/data_3002Annotation track

http://edamontology.org/data_0925Sequence assembly

MuGVREThe MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. It integrates genomics tools for chromatin dynamics data.https://www.multiscalegenomics.eu/mugvrebiotools:mugvre1.0Web applicationWorkbenchhttp://edamontology.org/topic_3176DNA packaginghttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_2275Molecular modellingPHPPythonApache-2.0RIS3CAT VEISFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3210Genome index

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2572BAM

http://edamontology.org/operation_0475Nucleic acid structure predictionhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2305GFF

http://edamontology.org/data_3870Trajectory data

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

http://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_3900DNA-binding protein predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2877Protein complexhttp://edamontology.org/format_1476PDB

http://edamontology.org/operation_3222Peak callinghttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAM

http://edamontology.org/data_1276Nucleic acid featureshttp://edamontology.org/format_3003BED

http://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_4002pickle

http://edamontology.org/data_0906Protein interaction datahttp://edamontology.org/format_4002pickle

http://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2084Nucleic acid report

http://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3870Trajectory data

http://edamontology.org/operation_0432Nucleosome position predictionhttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAM

http://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_2305GFF

http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/data_3869Simulationhttp://edamontology.org/data_0883Structurehttp://vre.multiscalegenomics.euServicehttps://github.com/Multiscale-Genomics/VRERepositoryhttps://www.multiscalegenomics.eu/MuGVRE/terms-of-use/Terms of usehttp://vre.multiscalegenomics.eu/help/starting.phpQuick start guidehttps://www.multiscalegenomics.eu/MuGVRE/training/Training materialnucleosome_dynamicsincludestadbitincludesjbrowseincludesnglincludes10.1101/602474Primary1.0Laia Codólaia.codo@bsc.eshttps://orcid.org/0000-0002-6797-8746PersonPrimary contactJosep Lluís Gelpíhttp://orcid.org/0000-0002-0566-7723PersonContributorMultiscale Complex Genomics Communityvre@multiscalegenomics.euhttps://www.multiscalegenomics.eu/ConsortiumDeveloperBioSurfDBBioSurfDB is a online database for biodegradation and biosurfactants.https://www.biosurfdb.orgbiosurfdbbiotools:biosurfdbDatabase portalhttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0821EnzymesMatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/data_2886Protein sequence record

http://edamontology.org/data_1383Nucleic acid sequence alignment

http://edamontology.org/data_1385Hybrid sequence alignment

http://edamontology.org/operation_0349Sequence database search (by property)

http://edamontology.org/data_1026Gene symbol

http://edamontology.org/data_1027Gene ID (NCBI)

http://edamontology.org/data_2299Gene name

http://edamontology.org/data_3494DNA sequence

10.1093/database/bav033PrimaryJorge S. Oliveirajorge.oliveira@tecnico.ulisboa.pthttps://web.tecnico.ulisboa.pt/jorge.oliveira/https://orcid.org/0000-0001-6425-2176PersonPrimary contactAna Teresa Freitasana.freitas@tecnico.ulisboa.pthttp://orcid.org/0000-0003-4638-2879PersonPrimary contactAna Tereza Ribeiro de Vasconcelosatrv@lncc.brhttp://orcid.org/0000-0002-4632-2086PersonPrimary contactLucymara Fassarella Agnez-Limalucymara.agnez@ufrn.brhttp://orcid.org/0000-0003-0642-3162PersonPrimary contactGil Poiares-Oliveiragpo@biodata.pthttps://web.tecnico.ulisboa.pt/gil.oliveirahttps://orcid.org/0000-0003-4638-2879PersonMaintainersamclipFilter SAM file for soft and hard clipped alignmentshttps://github.com/tseemann/samclipsamclipbiotools:samclip0.4.0Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0102MappingLinuxMacPerlhttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/data_1383Nucleic acid sequence alignment

http://edamontology.org/data_1383Nucleic acid sequence alignment

https://github.com/tseemann/samclipRepositoryhttps://anaconda.org/bioconda/samclipSoftware package0.4.0https://github.com/tseemann/samclipGeneralTREND Protein Evolution FunctionTREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.http://trend.evobionet.com/trend_protein_evolution_functionbiotools:trend_protein_evolution_functionWeb servicehttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/operation_0246Protein domain recognitionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_1900NCBI locus taghttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2385RefSeq accession (protein)

http://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_3464JSON

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3604SVG

http://edamontology.org/data_1245Sequence cluster (protein)http://edamontology.org/format_3464JSON

http://trend.evobionet.com/helpUser manual10.1093/nar/gkaa24332282909PMC7319448Primary10.1093/nar/gkac03435100406PMC8860576OtherCan be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937Vadim Gumerovgumerov.1@osu.eduhttps://orcid.org/0000-0003-1670-7679msaDisplay 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 contactCrispiA CRISPR Interactive database.http://crispi.genouest.org/crispibiotools:crispiDatabase portalhttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

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

A CRISPR Interactive databasehttp://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdfGeneral10.1093/bioinformatics/btp58619846435PMC2788928PrimaryGenOuestInstituteProviderGenOuest platformsupport@genouest.orghttp://www.genouest.orgPersonPrimary contactPlastParallel Local Alignment Search Tool for Database Comparison.http://www.irisa.fr/symbiose/projects/plast/plastbiotools:plast1.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCECILL-2.0MatureFree of chargehttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

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

Sequence alignmenthttps://plast.inria.fr/General10.1186/1471-2105-10-32919821978PMC2770072PrimaryGenOuestInstituteProviderDominique Lavenierlavenier@irisa.frPersonPrimary contactCyanoLyaseManually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.http://cyanolyase.genouest.org/cyanolyasebiotools:cyanolyaseDatabase portalhttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0858Sequence signature matcheshttp://edamontology.org/format_2330Textual format

Motif occurence detection in protein sequenceshttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1333BLAST results

Protein sequence alignment against known family membershttp://cyanolyase.genouest.org/helpGeneral10.1093/nar/gks109123175607PMC3531064PrimaryGenOuestInstituteProviderGenOuestsupport@genouest.orghttp://www.genouest.orgPersonPrimary contactSliderA suite of java classes which provides alignment of Illumina Sequence analyser reads. For alignment it uses base probabilities instead of sequences. It also enambles SNP prediction.http://www.bcgsc.ca/platform/bioinfo/software/slidersliderbiotools:sliderSuitehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_2533DNA mutationhttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowsMacJavaAFL-3.0http://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2959Nucleic acid probability profilehttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3033Matrix format

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_1921Alignment format

http://edamontology.org/data_0867Sequence alignment report

10.1093/bioinformatics/btn56518974170PMC2638935Slider supportnmalhis@bcgsc.caPersonPrimary contactwebPRANKMultiple sequence alignment tool.http://www.ebi.ac.uk/goldman-srv/webprank/webprankbiotools:webprank1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacGoldman ToolsEBI Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/goldman-srv/webprank/General10.1186/1471-2105-11-57921110866PMC3009689PrimaryGoldman groupPersonDeveloperAri LoytynojaPersonDeveloperNick GoldmanContributorEMBL-EBIInstituteProviderari@ebi.ac.ukPersonPrimary contactAri Loytynojaari.loytynoja@helsinki.fiPersonPrimary contactSASAnnotation of protein sequence with structural info from similar proteins in the PDB.http://www.ebi.ac.uk/thornton-srv/databases/sassasbiotools:sas1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_1476PDB

The ouput is an alignment of the query sequence vs a sequence from PDB, annotated by structural datahttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/sasGeneral10.1093/protein/11.10.8559862203PrimaryRoman LaskowskiPersonDeveloperThornton GroupPersonDeveloperDuncan MilburnContributorEMBL-EBIInstituteProviderroman@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactleBIBIpqpThe BioInformatics Prokaryotes Quick Phylogeny is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence. It is also giving the useful informations if species identification is needed.https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgilebibipqpbiotools:lebibipqp6.0Web applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacFree of chargehttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0258Sequence alignment analysishttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1056Database name

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

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/data_3272Species tree

http://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_1333BLAST results

https://umr5558-bibiserv.univ-lyon1.fr/BIBIDOCNEW/index.html#lebibi-qbpp-documentationGeneral10.1186/s12859-015-0692-z26264559PMC4531848IFB ELIXIR-FRInstituteProviderJean-Pierre Flandroisjean-pierre.flandrois@univ-lyon1.frPersonPrimary contactSeaViewMultiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences.http://doua.prabi.fr/software/seaviewseaviewbiotools:seaview4Command-line toolDesktop applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0084PhylogenyLinuxWindowsMachttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0326Phylogenetic tree editinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0540Phylogenetic tree generation (from molecular sequences)http://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0872Phylogenetic tree

http://edamontology.org/data_0872Phylogenetic tree

http://edamontology.org/data_0863Sequence alignment

http://edamontology.org/data_1707Phylogenetic tree image

http://edamontology.org/data_1711Sequence alignment image

http://doua.prabi.fr/software/seaviewSoftware cataloguehttp://doua.prabi.fr/main/indexGeneral10.1093/molbev/msp25919854763PrimaryIFB ELIXIR-FRInstituteProviderManolo Gouymgouy@biomserv.uni-lyon1.frPersonPrimary contactSWIPETool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.http://dna.uio.no/swipeswipebiotools:swipe2.0.5Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3047Molecular biologyLinuxC++AGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_2977Nucleic acid sequence

http://edamontology.org/data_1383Sequence alignment (nucleic acid)

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

https://github.com/torognes/swipeRepositoryhttps://github.com/torognes/swipeSource codehttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-221Citation instructionshttp://dna.uio.no/swipe/General10.1186/1471-2105-12-22121631914PMC3120707PrimaryTorbjørn RognesPersonDeveloperUiOInstituteProvidertorognes@ifi.uio.noPersonPrimary contactrnaSeqMapA library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time.http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.htmlrnaseqmapbiotools:rnaseqmap2.32.0Command-line toolLibraryhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacRGPL-2.0BioConductorhttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAM

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1921Alignment format

http://bioconductor/packages/release/bioc/src/contrib/rnaSeqMap_2.32.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/rnaSeqMap.htmlUser manual10.1186/1471-2105-12-20021612622PMC3128033PrimaryMichal Okoniewskimichal@fgcz.ethz.chPersonPrimary contactBSgenomeInfrastructure shared by all the Biostrings-based genome data packages.http://bioconductor.org/packages/release/bioc/html/BSgenome.htmlbsgenomebiotools:bsgenome1.42.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementLinuxWindowsMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1919Sequence record format

http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2330Textual format

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

http://bioconductor/packages/release/bioc/src/contrib/BSgenome_1.42.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/BSgenome.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherH. Pagèshpages@fredhutch.orgPersonPrimary contactRbowtieThis package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use QuasR instead of using this package directly.http://bioconductor.org/packages/release/bioc/html/Rbowtie.htmlrbowtiebiotools:rbowtie1.14.0Command-line toolLibraryhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacArtistic-1.0BioConductorhttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_1957rawhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_2573SAM

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2573SAM

http://bioconductor/packages/release/bioc/src/contrib/Rbowtie_1.14.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/Rbowtie.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherMichael Stadlermichael.stadler@fmi.chPersonPrimary contactgmapRGSNAP and GMAP are a pair of tools to align short-read data. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.http://bioconductor.org/packages/release/bioc/html/gmapR.htmlgmaprbiotools:gmapr1.16.0Command-line toolLibraryhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3170RNA-SeqLinuxWindowsMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1276Nucleic acid featureshttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2330Textual format

http://bioconductor/packages/release/bioc/src/contrib/gmapR_1.16.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/gmapR.htmlUser manual10.1007/978-1-4939-3578-9_1527008021PrimaryMichael Lawrencelawrence.michael@gene.comPersonPrimary contactBBCAnalyzerThis package visualizes the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.http://bioconductor.org/packages/release/bioc/html/BBCAnalyzer.htmlbbcanalyzerbiotools:bbcanalyzer1.4.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacRGPL-3.0BioConductorhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAM

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_1921Alignment formathttp://edamontology.org/format_2921Sequence variation annotation format

http://edamontology.org/data_2166Sequence composition plothttp://edamontology.org/format_1921Alignment formathttp://edamontology.org/format_2921Sequence variation annotation format

http://bioconductor/packages/release/bioc/src/contrib/BBCAnalyzer_1.4.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/BBCAnalyzer.htmlUser manual10.1186/s12859-017-1549-428241736PMC5330023PrimarySarah Sandmannsarah.sandmann@uni-muenster.dePersonPrimary contactbamsignalsThis package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.http://bioconductor.org/packages/release/bioc/html/bamsignals.htmlbamsignalsbiotools:bamsignals1.6.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacRGPL-2.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAM

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_1921Alignment format

http://bioconductor/packages/release/bioc/src/contrib/bamsignals_1.6.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/bamsignals.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherAlessandro Mammanamammana@molgen.mpg.dePersonPrimary contactBaseSpaceRA rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.http://bioconductor.org/packages/release/bioc/html/BaseSpaceR.htmlbasespacerbiotools:basespacer1.18.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3372Software engineeringLinuxWindowsMacRApache-2.0BioConductorhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_3016VCF

http://bioconductor/packages/release/bioc/src/contrib/BaseSpaceR_1.18.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/BaseSpaceR.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherJared O'Connelljoconnell@illumina.comPersonPrimary contactUniProt AlignMultiple sequence alignment.http://www.uniprot.org/alignuniprot_alignbiotools:uniprot_align1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCC-BY-ND-3.0UniProt ToolsEBI Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0863Sequence alignment

http://www.uniprot.org/contactHelpdeskhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.uniprot.org/help/sequence-alignmentsGeneralhttp://www.uniprot.org/help/licenseTerms of use10.1093/nar/gku98925348405PMC4384041PrimaryUniProt Consortiumhttp://www.uniprot.org/help/aboutInstituteProviderEMBL-EBIhttp://www.ebi.ac.uk/InstituteProviderhttp://www.uniprot.org/contactPersonPrimary contactXavier Watkinswatkins@ebi.ac.ukPersonPrimary contactPickyA pipeline for detecting structural variants from third generation long read sequencing data (works on Oxford Nanopore and PacBio).https://github.com/TheJacksonLaboratory/Pickypickybiotools:pickyCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_2640OncologyLinuxMacPerlMatureFree of chargehttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3228Structural variation detectionhttp://edamontology.org/data_3497DNA sequence (raw)http://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2573SAM

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

https://github.com/TheJacksonLaboratory/PickySoftware packageA Github page.https://github.com/TheJacksonLaboratory/Picky/wikiGeneralA Github wiki10.1038/s41592-018-0002-629713081PMC5990454Chia-Lin Weihttps://www.nature.com/articles/s41592-018-0002-6/email/correspondent/c1/newPersonPrimary contactcellAlignA method for comparing expression dynamics within and between single-cell differentiation trajectories.https://github.com/shenorrLab/cellAligncellalignbiotools:cellalignPlug-inhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3064Developmental biologyWindowsROtherMatureFree of chargehttp://edamontology.org/operation_3439Pathway or network predictionhttp://edamontology.org/operation_3223Differential gene expression analysishttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_2337Resource metadatahttp://edamontology.org/format_3326Data index format

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_2032Workflow format

https://github.com/shenorrLab/cellAlignSoftware packagehttps://github.com/shenorrLab/cellAlignGeneral10.1038/nmeth.462829529018Ayelet Alperthttps://www.linkedin.com/in/ayelet-alpert-5a525167/PersonPrimary contactBiostringsMemory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.http://bioconductor.org/packages/release/bioc/html/Biostrings.htmlbiostringsbiotools:biostrings2.42.1Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementLinuxWindowsMacRArtistic-2.0BioConductorFree of chargehttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_3115Microarray metadatahttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/format_1919Sequence record format

http://edamontology.org/data_3115Microarray metadatahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2330Textual format

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

http://bioconductor/packages/release/bioc/src/contrib/Biostrings_2.42.1.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/Biostrings.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherH. Pagèshpages@fredhutch.orgPersonPrimary contactPhymyco-DBA database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses.http://phymycodb.genouest.org/phymyco-dbbiotools:phymyco-dbDatabase portalhttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacFree of chargehttp://edamontology.org/operation_2928Alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTA

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

Sequence alignmenthttp://phymycodb.genouest.org/General10.1371/journal.pone.004311723028445PMC3441585PrimaryGenOuestInstituteProviderGenOuestsupport@genouest.orgPersonPrimary contactEnsembl Genomes Fungi sequence searchSearches Ensembl Fungi sequences using Exonerate.http://fungi.ensembl.org/Multi/enasearchensembl_genomes_fungi_sequence_searchbiotools:ensembl_genomes_fungi_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://edamontology.org/data_0857Sequence search results

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://fungi.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Protists sequence searchSearches Ensembl Protists sequences using Exonerate.http://protists.ensembl.org/Multi/enasearchensembl_genomes_protists_sequence_searchbiotools:ensembl_genomes_protists_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://protists.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Metazoa sequence searchSearches Ensembl Metazoa sequences using Exonerate.http://metazoa.ensembl.org/Multi/enasearchensembl_genomes_metazoa_sequence_searchbiotools:ensembl_genomes_metazoa_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://metazoa.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl Genomes teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Plants sequence searchSearch Ensembl Plants sequences with Exonerate.http://plants.ensembl.org/Multi/enasearchensembl_genomes_plants_sequence_searchbiotools:ensembl_genomes_plants_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://edamontology.org/data_0857Sequence search results

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://plants.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl Genomes teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactEnsembl Genomes Bacteria sequence searchSearches Ensembl Bacteria sequences using Exonerate.http://bacteria.ensembl.org/Multi/enasearchensembl_genomes_bacteria_sequence_searchbiotools:ensembl_genomes_bacteria_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacEnsembl ToolsEnsembl GenomesEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://edamontology.org/data_0857Sequence search results

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://bacteria.ensembl.org/info/website/help/index.htmlGeneral10.1093/nar/gkv115726687719PMC4702834OtherEnsembl Genomes teamPersonDeveloperEMBL-EBIInstituteProviderhelpdesk@ensemblgenomes.orgPersonPrimary contactEnsembl Genomes webteameg-webteam@ebi.ac.ukPersonPrimary contactProDom protein domain databaseA comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.http://prodom.prabi.fr/prodom/current/html/home.phpprodombiotools:prodomDatabase portalhttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacDRCATDataFrancehttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1142ProDom accession number

http://edamontology.org/data_0907Protein family reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1142ProDom accession number

http://edamontology.org/data_1384Sequence alignment (protein)http://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1142ProDom accession number

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1142ProDom accession number

http://edamontology.org/data_1276Nucleic acid featureshttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1142ProDom accession number

http://edamontology.org/data_1384Sequence alignment (protein)http://edamontology.org/format_2330Textual format

http://prodom.prabi.fr/prodom/current/documentation/help.phpGeneral10.1093/nar/28.1.26710592243PMC102458PrimaryDRCATProjectDocumentorhttp://prodom.prabi.fr/prodom/current/html/prodom_team.phpPersonPrimary contactantgenomes.orgCommunity database centralizing genomic and transcriptomic sequence information for ants and related species (e.g., bees and wasps). Provides BLAST search and data download. Updated periodically with latest data and new tools.http://antgenomes.organtgenomes.orgbiotools:antgenomes.orgDatabase portalhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308TranscriptomicsLinuxWindowsMacWurmLabhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_2200FASTA-like (text)

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_2331HTML

http://antgenomes.org/General10.1186/1471-2164-10-519126223PMC2639375PrimaryWurmLabDivisionDeveloperYannick Wurmy.wurm@qmul.ac.ukPersonPrimary contactClustalO WS (jabaws)JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview.http://www.compbio.dundee.ac.uk/jabawsclustalo_ws_jabawsbiotools:clustalo_ws_jabaws1Web servicehttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavaclustalJABAWShttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTA

https://www.biocatalogue.org/services/3687Software cataloguehttp://www.compbio.dundee.ac.uk/jabaws/man_about.htmlUser manualhttp://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/ClustalOWS.htmlAPI documentation10.1093/bioinformatics/btr30421593132PMC3129525PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://www.compbio.dundee.ac.uk/jabaws/contacts.htmlPersonPrimary contact