PAL2NALPAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.http://www.bork.embl.de/pal2nal/pal2nalbiotools:pal2nalWeb applicationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacPerlhttp://edamontology.org/operation_0550DNA substitution modellinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0292Sequence alignment10.1093/nar/gkl31516845082PMC1538804Mikita Suyamamikita@bioreg.kyushu-u.ac.jpPersonPrimary contactTherapeutic Nanobody Profiler (TNP)The Therapeutic Nanobody Profiler (TNP) is an open-source computational tool designed to predict nanobody developability, accounting for their unique properties compared to conventional antibodies. It is accessible as a web application and provides tailored metrics for more efficient nanobody development.http://opig.stats.ox.ac.uk/webapps/tnptnpbiotools:tnphttp://edamontology.org/topic_3374Biotherapeuticshttp://edamontology.org/topic_2830Immunoproteins and antigenshttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_2518Nucleic acid structure comparison10.1101/2025.08.11.669635MAFcounterMAFcounter is a tool for counting k-mers in Multiple Alignment Format (MAF) files, designed to address a previously unmet need in bioinformatics. The software is multithreaded, fast, and memory efficient, making it suitable for large-scale sequence alignment analysis.https://github.com/Georgakopoulos-Soares-lab/MAFcountermafcounterbiotools:mafcounterhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0081Structure analysisC++GPL-3.0http://edamontology.org/operation_3182Genome alignmenthttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysis10.1186/S12859-025-06172-740448014PMC12125892Ioannis Mouratidisioannis.mouratidis@psu.eduPersonIlias Georgakopoulos-Soaresizg5139@psu.eduPersonMDTAPMDTAP is a Linux/Mac-based software that automatically detects permeation events across membrane-embedded protein and nucleic acid channels from molecular dynamics simulation trajectories. It accepts DCD and PDB formats and is freely available on GitHub.https://github.com/MBL-lab/MDTAPmdtapbiotools:mdtaphttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_0154Small moleculesBashhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_2476Molecular dynamics10.1093/BIOADV/VBAF10240421423PMC12104522Thenmalarchelvi Rathinavelantr@bt.iith.ac.inhttps://orcid.org/0000-0002-1142-0583PersonGenomic SSR Millets Database (GSMDB)The Genomic SSR Millets Database (GSMDB) is a web-based resource providing comprehensive details on over 6.7 million Simple Sequence Repeats (SSRs) mined from the genomic sequences of seven millet species. It aims to facilitate millet cultivar advancement and related research, contributing to global food security.https://bioinfo.icgeb.res.in/gsmdb/gsmdbbiotools:gsmdbhttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3390Nutritional sciencehttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0237Repeat sequence analysis10.1093/DATABASE/BAAE11439546404PMC11566590Dinesh Guptadinesh@icgeb.res.inhttps://orcid.org/0000-0002-7548-8835PersonFastOMAFastOMA is a scalable software package to infer orthology relationship.https://github.com/dessimozlab/FastOMAfastomabiotools:fastoma0.5.1Command-line toolhttp://edamontology.org/topic_0797Comparative genomicsMacLinuxPythonMPL-2.0MatureFree of chargeOpen accessSwitzerlandhttp://edamontology.org/operation_3947Phylogenetic tree reconciliationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3209Genome comparisonhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0540Phylogenetic inference (from molecular sequences)http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1910newick

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

http://edamontology.org/data_3148Gene family reporthttp://edamontology.org/format_3850OrthoXML

https://github.com/dessimozlab/FastOMARepositoryhttps://omabrowser.orgServicehttps://github.com/DessimozLab/FastOMA/blob/main/README.mdQuick start guideomameruses10.1038/s41592-024-02552-839753922PMC11810774seqfuA collection of utilities to manipulate FASTA and FASTQ files, supporting Gzipped input.https://telatin.github.io/seqfu2/seqfubiotools:seqfu1.10.01.11.01.12.01.13.01.14.01.15.01.16.01.17.01.19.01.20.01.21.01.22.01.22.3Command-line toolhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_2977Nucleic acid sequence

seqfu [subcommand] FASTX > FASTXhttps://telatin.github.io/seqfu2OtherDocumentationhttps://github.com/telatin/seqfu2/Repositoryhttps://github.com/telatin/seqfu2Software packagehttps://github.com/telatin/seqfu2/releasesDownloads pagehttps://bioconda.github.io/recipes/seqfu/README.htmlSoftware package1.0.0-1.22.3https://telatin.github.io/seqfu2/User manual10.3390/bioengineering805005934066939PMC8148589Primary1.0South Green Genome HubsThe South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).https://banana-genome-hub.southgreen.fr/South_Green_Genome_Hubsbiotools:South_Green_Genome_HubsDatabase portalhttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0621Model organismsJavaScriptPHPGPL-2.0Genome HubMatureFree of chargeDataToolsFrancehttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2044Sequence

https://github.com/SouthGreenPlatform/genomehubsIssue trackerhttps://banana-genome-hub.southgreen.fr/content/term-serviceTerms of usetripalusesbanana_genome_hubincludescoffee_genome_hubincludescocoa_genome_hubincludesrice_genome_hubincludessugarcane_genome_hubincludessouthgreenincludedIn10.1093/database/bat03523707967PMC3662865Primary10.1093/nar/gku110825392413PMC4383925Primary10.1093/hr/uhac22136479579PMC9720444Primary10.1016/j.xplc.2022.10033035617961PMC9482989UsageGaetan Drocdroc@cirad.frhttps://orcid.org/0000-0003-1849-1269PersonPrimary contactDeveloperDocumentorProviderSupportAlexis Dereeperalexis.dereeper@ird.frMathieu Rouardm.rouard@cgiar.orghttps://orcid.org/0000-0003-1849-1269Primary contactMaintainerSupportValentin Guignonv.guignon@cgiar.orgChrisitine Tranchantchristine.tranchant@ird.frStéphanie Bocsstephanie.sidibe-bocs@cirad.frDISULFINDDISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.http://disulfind.dsi.unifi.it/disulfindbiotools:disulfindWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_1850Protein cysteine and disulfide bond assignmenthttp://edamontology.org/operation_3092Protein feature detectionhttp://disulfind.dsi.unifi.it/help.phpGeneral10.1093/nar/gkl26616844986PMC153882310.1093/bioinformatics/btg4631503387210.1093/nar/gkr36521576237PMC312577110.1093/bioinformatics/btn37118635571PMC2732205DISULFIND Supportdisulfind@ai.dinfo.unifi.itPersonPrimary contactMASSPECMASSPEC is (or was) a computer program for the complete sequence analysis of large proteins from a single mass spectrum, a precursor to modern-day software for de novo sequencing and top-down proteomics.https://doi.org/10.1016/0010-4825(70)90013-2masspecbiotools:masspecCommand-line toolhttp://edamontology.org/topic_0121ProteomicsFortranLegacyhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2330Textual format

10.1016/0010-4825(70)90013-25524587PrimaryComproteinComprotein is (or was) a computer program to aid in primary protein structure determination, i.e. protein sequencing.https://dl.acm.org/doi/10.1145/1461518.1461546comproteinbiotools:comproteinFortranLegacyhttp://edamontology.org/operation_2479Protein sequence analysis10.1145/1461518.1461546PrimaryfastplongUltrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).https://github.com/OpenGene/fastplongfastplongbiotools:fastplongCommand-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0080Sequence analysisMITFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3218Sequencing quality controlhttps://github.com/OpenGene/fastplongRepositoryhttps://github.com/OpenGene/fastplong/issuesIssue tracker10.1002/imt2.10738868435PMC10989850MethodMentioned as Citation in the git repository. Publication describes only the (short read) tool fastp.OpenGenehttps://github.com/OpenGeneOpenGene - Open Source Genomics Toolbox Open source tools for NGS data analysisREPETThe REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.https://urgi.versailles.inrae.fr/Tools/REPETrepetbiotools:repetv3.0Command-line toolhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacC++PythonCECILL-2.0REPETelixir-fr-sdp-2019URGILegacyFree of chargeOpen accessToolsFrancehttp://edamontology.org/operation_0379Repeat sequence detectionhttp://edamontology.org/operation_0237Repeat sequence analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTA

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

http://edamontology.org/data_1270Feature tablehttp://edamontology.org/format_2206Sequence feature table format (text)

http://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_1939GFF3-seq

https://urgi.versailles.inrae.fr/download/repet/Repositoryhttps://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gzSource codev3.0https://urgi.versailles.inrae.fr/Tools/REPETGeneralsee also https://urgi.versailles.inrae.fr/Tools/REPET/READMEhttps://urgi.versailles.inrae.fr/Tools/REPET/INSTALLInstallation instructionshttps://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tutoUser manualSee also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tutohttps://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorialTraining material10.1371/journal.pone.009192924786468PMC4008368Primary10.1371/journal.pone.001652621304975PMC3031573Primary10.1371/journal.pcbi.001002216110336PMC1185648Primary10.1007/s00239-003-0007-215008403Method10.1109/JPROC.2016.2590833MethodURGIurgi-repet@versailles.inrae.frhttp://urgi.versailles.inrae.fr/InstituteDeveloperContributorMaintainerProviderSupportDocumentorThis tool has a "Numero de depot APP": FR 001 480007 000 R P 2008 000 31 235EukRepClassification of Eukaryotic and Prokaryotic sequences from metagenomic datasetshttps://github.com/patrickwest/EukRepeukrepbiotools:eukrepCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsPythonMIThttp://edamontology.org/operation_2478Nucleic acid sequence analysis10.1101/gr.228429.117SILVAngsSILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download.https://ngs.arb-silva.desilvangsbiotools:silvangs1.9.10Web applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3697Microbial ecologyde.NBIde.NBI-biodataDSMZ Digital DiversityMatureFree of charge (with restrictions)DataGermanyhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3475TSV

http://edamontology.org/data_2884Plot

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3508PDF

http://edamontology.org/data_1246Sequence cluster (nucleic acid)http://edamontology.org/format_1984FASTA-aln

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

The pipeline accepts input data in Multi-Fasta format with each input file representing one sample. Samples that belong to one project (a transect, timeseries etc.) should be uploaded as a single SILVAngs project.https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdfUser manualhttps://www.arb-silva.de/documentation/silvangs/userfaq/FAQhttps://www.arb-silva.de/footer/sngs-termsofuseTerms of usesilvauses10.1093/nar/gks121923193283PMC3531112Primary10.1093/nar/gkt120924293649PMC3965112Primary10.1093/bioinformatics/bts25222556368PMC3389763PrimarySILVA Teamngs-contact@arb-silva.dehttps://www.arb-silva.de/contact/team/grid.507782.f027z9pz32DivisionPrimary contactLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshub@dsmz.dehttps://www.dsmz.degrid.420081.f02tyer376InstituteProviderNanoPackVisualizing and processing long-read sequencing data.https://github.com/wdecoster/nanopacknanopackbiotools:nanopack1.1.0Command-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxMacPythonVIBhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0564Sequence visualisationhttps://github.com/wdecoster/nanopackGeneralnanoplotincludes10.1093/bioinformatics/bty14929547981PMC6061794Wouter De Costerwouter.decoster@molgen.vib-ua.bePersonPrimary contactMuGVREThe 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/ConsortiumDeveloperneXtProtneXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.https://www.expasy.org/archives/nextprotnextprotbiotools:nextprotDatabase portalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_3120Protein variantshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacCC-BY-4.0Rare DiseaseProteomicsLegacyFree of chargeDataSwitzerlandhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_2406Protein structure analysishttps://github.com/calipho-sib/RepositoryneXtProt software repository with issue trackinghttps://twitter.com/nextprot_newsSocial medianeXtProt release news, publications, presentations, tips and more. DM us with feedback!https://www.expasy.org/resources/nextprotSoftware catalogueneXtProt entry in Expasy10.1093/nar/gkz99531724716Primary10.1093/nar/gkr117922139911PMC3245017PrimarySIB Swiss Institute of BioinformaticsInstituteProviderSupportsupport@nextprot.orgPersonPrimary contactPascale Gaudethttp://orcid.org/0000-0003-1813-6857PersonContributorSIMAP WSDatabase containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes.http://liferay.csb.univie.ac.at/portal/web/simap/webservicesimap_wsbiotools:simap_ws1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2479Protein sequence analysishttps://www.biocatalogue.org/services/3726Software cataloguehttp://liferay.csb.univie.ac.at/portal/web/simap/webserviceGeneral10.1093/nar/gkj10616381858PMC1347468PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://liferay.csb.univie.ac.at/portal/web/simap/contactPersonPrimary contactRNAalifoldWSPredict a consensus secondary structure of a set of aligned sequences.http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgirnaalifoldwsbiotools:rnaalifoldws1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttps://www.biocatalogue.org/services/3717Software cataloguehttp://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgiGeneral10.1186/1471-2105-9-47419014431PMC2621365PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorhttp://www.compbio.dundee.ac.uk/jabaws/contacts.htmlPersonPrimary contactIBM Bioinformatics and Pattern Discovery GroupExtensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.http://cbcsrv.watson.ibm.com/Tspd.htmlibm_pattern_discoverybiotools:ibm_pattern_discoveryWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/operation_0452Indel detectionhttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3761Service discoveryhttp://edamontology.org/operation_0238Sequence motif discovery10.1093/nar/gkf33812060689PMC11728110.1093/bioinformatics/14.1.55952050210.1093/nar/gkg62112824385PMC16902710.1093/nar/gkf46412202776PMC13740510.1006/mben.2000.01511105605910.1093/nar/gkh36715215340PMC44150510786305REPPERTool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats.http://protevo.eb.tuebingen.mpg.de/repperrepperbiotools:repperWeb applicationhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/operation_0379Repeat sequence detectionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0380Repeat sequence organisation analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3092Protein feature detection10.1093/nar/gki40515980460PMC1160166SeLOXWeb server identifies degenerate lox-like sites within genomic sequences.http://selox.mpi-cbg.de/cgi-bin/selox/indexseloxbiotools:seloxWeb applicationhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_2815Humanshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/operation_3209Genome comparisonhttp://edamontology.org/operation_0451Recombination detectionhttp://edamontology.org/operation_0237Repeat sequence analysis10.1093/nar/gkq52320529878PMC2896191TarOCollection of tools for protein target optimization analysis. Tools include those for annotation of putative orthologues and homologues, searches against the PDB with PSIBLAST, generation of annotated multiple sequence alignments and presentation of integrated results.http://www.compbio.dundee.ac.uk/tarotarobiotools:taroWeb applicationhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0303Protein fold recognition10.1093/nar/gkn14118385152PMC2447720CRISPRcomparClustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in this tool as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.http://crispr.u-psud.fr/CRISPRcompar/crisprcomparbiotools:crisprcomparWeb applicationhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0237Repeat sequence analysis10.1093/nar/gkn22818442988PMC2447796PARSESNPTool for the analysis of polymorphisms in genes.http://www.proweb.org/parsesnp/parsesnpbiotools:parsesnpWeb applicationhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_3202Polymorphism detectionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_0477Protein modelling10.1093/nar/gkg57412824424PMC168980hmmstat (genouest)Display summary statistics for a profile file.http://webservices.genouest.org/opal2/dashboard?command=docshmmstat_genouestbiotools:hmmstat_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2479Protein sequence analysishttps://www.biocatalogue.org/services/2735Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmsim (genouest)Collect profile HMM score distributions on random sequences.http://webservices.genouest.org/opal2/dashboard?command=docshmmsim_genouestbiotools:hmmsim_genouest1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2734Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773ReviewBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmsearch (genouest)Search profile(s) against a sequence database.http://webservices.genouest.org/opal2/dashboard?command=docshmmsearch_genouestbiotools:hmmsearch_genouest1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2733Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773ReviewBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmscan (genouest)Search sequence(s) against a profile database.http://webservices.genouest.org/opal2/dashboard?command=docshmmscan_genouestbiotools:hmmscan_genouest1Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2732Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmfetch (genouest)Retrieve profile HMM(s) from a file.http://webservices.genouest.org/opal2/dashboard?command=docshmmfetch_genouestbiotools:hmmfetch_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2731Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmemit (genouest)Sample sequence(s) from a profile HMM.http://webservices.genouest.org/opal2/dashboard?command=docshmmemitbiotools:hmmemit1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2730Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmconvert (genouest)Convert between profile HMM file formats.http://webservices.genouest.org/opal2/dashboard?command=docshmmconvert_genouestbiotools:hmmconvert_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2729Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1006/jmbi.1994.11048107089OtherBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contacthmmalign (genouest)Align sequences to a profile HMM.http://webservices.genouest.org/opal2/dashboard?command=docshmmalign_genouestbiotools:hmmalign_genouest1Web servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisGenOuesthttp://edamontology.org/operation_2403Sequence analysishttps://www.biocatalogue.org/services/2727Software cataloguehttp://webservices.genouest.org/opal2/dashboard?command=docsGeneral10.1093/nar/gkr36721593126PMC3125773PrimaryBioCataloguehttps://www.biocatalogue.orgProjectDocumentorsupport@genouest.orgPersonPrimary contactPicXAA-WebWeb tool for probablistic alignment of multiple biological sequences using probabilistic non-progressive alignment algorithms. Multiple protein, DNA and RNA sequences may be analyzed.http://gsp.tamu.edu/picxaa/picxaa-webbiotools:picxaa-webWeb applicationhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/operation_0499Tree-based sequence alignmenthttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0292Sequence alignment10.1093/nar/gkr24421515632PMC3125727PiRaNhAPredicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.http://www.bioinformatics.sussex.ac.uk/PIRANHApiranhabiotools:piranhaWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/operation_0272Residue interaction predictionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0267Protein secondary structure prediction10.1093/nar/gkq47420507911PMC289609910.1093/bioinformatics/btp25719389733PlotRepTool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output.http://repeats.abc.hu/cgi-bin/plotrep.plplotrepbiotools:plotrepWeb applicationhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/operation_0237Repeat sequence analysis10.1093/nar/gkl26316845104PMC1538846ProteoMirExpressWeb server that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks.http://jjwanglab.org/proteomirexpress/proteomirexpressbiotools:proteomirexpressWeb applicationhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2497Pathway or network analysishttp://www.mybiosoftware.com/proteomirexpress-inferring-microrna-and-protein-centered-regulatory-networks.htmlSoftware cataloguehttp://jjwanglab.org/proteomirexpress/helpGeneral10.1074/mcp.o112.01985123924514PMC3820948http://jjwanglab.org/proteomirexpress/aboutPersonPrimary contactPOPDISTNewly-developed population genetic data analysis program. It calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures.http://genetics.agrsci.dk/~bernt/popgen/popdistbiotools:popdistCommand-line toolhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3056Population geneticsLinuxWindowsMachttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3478Phylogenetic tree reconstructionhttp://www.mybiosoftware.com/popdist-1-2-3-population-genetic-data-analysis-program.htmlSoftware cataloguehttp://genetics.agrsci.dk/~bernt/popgen/#docGeneral10.1111/j.1755-0998.2009.02623.x21564908http://pure.au.dk/portal/en/persons/id(782adba8-3ec8-409b-afd7-81f2d75579b2).htmlPersonPrimary contactRDC-PANDARDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. It is specifically designed for automated NMR NOE assignment and protein structure determination.http://www.cs.duke.edu/donaldlab/rdcpanda.phprdc-pandabiotools:rdc-pandaSuitehttp://edamontology.org/topic_0593NMRhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/rdc-panda-1-0-nmr-noe-assignment-protein-structure-determination.htmlSoftware cataloguehttp://www.cs.duke.edu/donaldlab/software/rdcpanda/rdc-panda_manual.pdfUser manual10.1007/s10858-009-9366-319711185PMC2766249panda@cs.duke.eduhttp://www.cs.duke.edu/donaldlab/index.phpPersonPrimary contactI-PVSoftware that uses Circos to render interactive images for protein sequence visualization.http://www.i-pv.org/i-pvbiotools:i-pvWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0337Visualisationhttp://www.mybiosoftware.com/i-pv-circos-module-for-interactive-protein-sequence-visualization.htmlSoftware cataloguehttp://www.i-pv.org/#nutShellGeneral10.1093/bioinformatics/btv57926454277Ibrahim Tanyalcinibrahim.tanyalcin@i-pv.orghttp://www.i-pv.org/aboutMe.htmlPersonPrimary contact14-3-3-PredWebserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM.http://www.compbio.dundee.ac.uk/1433pred1433predbiotools:1433predWeb applicationhttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2575Protein binding site predictionhttp://www.mybiosoftware.com/14-3-3-pred-webserver-to-predict-14-3-3-binding-sites-in-proteins.htmlSoftware cataloguehttp://www.compbio.dundee.ac.uk/1433pred/aboutGeneral10.1093/bioinformatics/btv13325735772PMC4495292The Barton Grouphttp://www.compbio.dundee.ac.uk/contact.htmlPersonPrimary contactiMem-SeqMulti-label classifier for identifying membrane proteins with single and multiple types via physical-chemical property matrix and grey-PSSM.http://www.jci-bioinfo.cn/iMem-Seqimem-seqbiotools:imem-seqWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/imem-seq-predicting-membrane-proteins-types.htmlSoftware cataloguehttp://www.jci-bioinfo.cn/iMem/iMem_readme.htmlGeneral10.1007/s00232-015-9787-825796484Xiao Xuanjdzxiaoxuan@163.comhttp://www.jci-bioinfo.cn/PersonPrimary contactPutracerReliable method to detect automatically structural domains as protein units. This server provides number of domains and domain boundary for a chain with continues-domains.http://bioinf.modares.ac.ir/software/PUTracer/putracerbiotools:putracerWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2406Protein structure analysishttp://www.mybiosoftware.com/putracer-protein-unit-tracer.htmlSoftware cataloguehttp://bioinf.modares.ac.ir/software/PUTracer/General10.1142/s021972001340012x23427994sh.arab@modares.ac.irPersonPrimary contactPPCMatrixVersatile dotmatrix program for the Apple Macintosh, optimized for the PowerPC.http://www.bionut.ki.se/groups/tbu/software/#PPCMatrixppcmatrixbiotools:ppcmatrixDesktop applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0602Molecular interactions, pathways and networksMachttp://edamontology.org/operation_2451Sequence comparisonhttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/ppcmatrix-1-25-dotmatrix-program-compare-large-genomic-sequences-protein-sequences.htmlSoftware cataloguehttp://www.bionut.ki.se/groups/tbu/software/ppcmatrixinfo.htmlGeneral10.1093/oxfordjournals.bioinformatics.a0110559789102thomas.burglin@biosci.ki.sePersonPrimary contactHMMpTMHidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence.http://aias.biol.uoa.gr/HMMpTM/hmmptmbiotools:hmmptmWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0820Membrane and lipoproteinsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://www.mybiosoftware.com/hmmptm-transmembrane-protein-topology-prediction-using-phosphorylation-and-glycosylation-site-prediction.htmlSoftware cataloguehttp://aias.biol.uoa.gr/HMMpTM/about.phpUser manual10.1016/j.bbapap.2013.11.00124225132Biophysics & Bioinformatics Laboratorybiophysics@biol.uoa.grhttp://biophysics.biol.uoa.gr/PersonPrimary contactPrinceton_TIGRESSAutomated refinement method that intends to refine an input protein structure by addressing both sampling and selection.http://atlas.princeton.edu/refinement/princeton_tigressbiotools:princeton_tigressWeb applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0130Protein folding, stability and designLinuxWindowsMachttp://edamontology.org/operation_2415Protein folding analysishttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/princeton_tigress-protein-geometry-refinement-using-simulations-and-support-vector-machines.htmlSoftware cataloguehttp://atlas.engr.tamu.edu/refinement/General10.1002/prot.2445924174311Christodoulos A. Floudasfloudas@titan.princeton.eduPersonPrimary contactPocketDepthAlgorithm for finding binding site (pockets) in protein structures.http://proline.physics.iisc.ernet.in/pocketdepth/pocketdepthbiotools:pocketdepthWeb applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2575Protein binding site predictionhttp://www.mybiosoftware.com/pocketdepth-a-new-depth-based-algortihm-for-identification-of-ligand-binding-sites.htmlSoftware cataloguehttp://proline.physics.iisc.ernet.in/pocketdepth/other_info/algorithm.htmlGeneral10.1016/j.jsb.2007.09.00517949996http://proline.physics.iisc.ernet.in/pocketdepth/other_info/contact.htmlPersonPrimary contactAAIndexLocMachine-learning-based algorithm that uses amino acid index to predict protein subcellular localization based on its sequence.http://aaindexloc.bii.a-star.edu.sg/aaindexlocbiotools:aaindexlocWeb servicehttp://edamontology.org/topic_0140Protein targeting and localisationLinuxWindowsMachttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/aaindexloc-predicting-protein-subcellular-localization-using-amino-acid-index.htmlSoftware cataloguehttp://aaindexloc.bii.a-star.edu.sg/General10.1007/s00726-007-0616-y18163182http://www.bii.a-star.edu.sg/PersonPrimary contactAsymmetryAmbiguityRemover removes ambiguously aligned sites from protein sequence alignments, for input into AsymmetryCounter. AsymmetryCounter counts the number of amino acid substitutions in each direction between pairs of protein sequences. AsymmetryScaler takes the results from AsymmetryCounter and summarizes substitutional asymmetry data in a single scale.http://udel.edu/~mcdonald/asymmetry.htmlasymmetrybiotools:asymmetryDesktop applicationhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0080Sequence analysisWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/asymmetry-20060215-test-protein-sequence-data-substitutional-asymmetry.htmlSoftware cataloguehttp://udel.edu/~mcdonald/asymmetry.htmlSoftware cataloguehttp://udel.edu/~mcdonald/asymmetry.htmlGeneral10.1093/oxfordjournals.molbev.a02609010605119McDonald, J.Hmcdonald@udel.eduhttp://udel.edu/~mcdonald/PersonPrimary contact