trimAlTool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.http://trimal.cgenomics.orgtrimalbiotools:trimal1.42.0-RCCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacC++MatureFree of chargehttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1998phylipnonhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2330Textual formathttps://github.com/inab/trimalRepositoryhttps://github.com/inab/trimalSource code1.4https://github.com/inab/trimal/tree/2.0_RCSource code2.0-RChttp://trimal.cgenomics.org/GeneralVersion 1.2https://trimal.readthedocs.ioGeneralVersion 1.4 and 2 (not updated)19505945Salvador Capella-Gutierrezsalcagu@gmail.comPersonPrimary contacttgabaldon@crg.eshttp://gabaldonlab.crg.es/PersonPrimary contactJalviewJalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to 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:Jalview2.11.3.2Desktop applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacGPL-3.0ELIXIR-UKMatureFree of chargeOpen accessToolsUKhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1939GFF3-seqhttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_1938GFF2-seqhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3311RNAMLhttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1947GCG MSFhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_2884Plothttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3466EPShttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_1915FormatOther 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://source.jalview.org/crucible/browse/jalviewRepositoryhttps://twitter.com/JalviewSocial mediaTwitter feedhttps://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfwSocial mediaYouTube training videoshttps://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-beaconsusesuniprotusespfamusesensemblusespdbusesrfamuses10.1093/bioinformatics/btp033Jim 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/0000-0002-9014-5355kc-alignA fast and accurate tool for performing codon-aware multiple sequence alignmentshttps://github.com/davebx/kc-alignkc-alignbiotools:kc-align1.0Command-line toolhttp://edamontology.org/topic_0102MappingAFL-3.0Open accesshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1929FASTAkc-align -m genome -r reference.fasta -S sequences.fasta -s 3532,3892 -e 3894,5326MUSCLEThis tool performs multiple sequence alignments of nucleotide or amino acid sequences.https://www.drive5.com/muscle/musclebiotools:muscle5Command-line toolWeb APIhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacOtherMUSCLEgalaxyPasteurBioConductorMatureFree of chargeOpen accesshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_3494DNA 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_3495RNA 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_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/format_1929FASTAhttps://www.biocatalogue.org/services/3135Software cataloguehttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/muscle/3.8.31.1Galaxy servicehttp://bioconductor/packages/release/bioc/src/contrib/muscle_3.16.0.tar.gzSource codeBioConductor packagehttps://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_restAPI specificationEBI MUSCLE Web Servicehttps://www.drive5.com/muscle/downloads.htmDownloads pagehttp://bioconductor.org/packages/release/bioc/html/muscle.htmlUser manualBioConductor package documentationhttps://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_restAPI documentationEBI Web Service documentationhttps://www.drive5.com/muscle/manual/User manualhttps://www.drive5.com/muscle/manual/install.htmlInstallation instructions10.1093/nar/gkh34015034147PMC390337Primary10.7490/f1000research.1114334.1Other10.1186/1471-2105-5-113Other10.1101/2021.06.20.449169Primary5Alex T. Kalinkaalex.t.kalinka@gmail.comPersonMaintainerMaintainer of the BioConductor packagehttp://www.ebi.ac.uk/support/PersonPrimary contactEBI Web Service supportTechnical Supporthttps://www.drive5.com/muscle/manual/support.htmlRobert Edgarrobert@drive5.comPersonPrimary contactDeveloperClustalW (BioLib)ClustalW is a general purpose multiple sequence alignment program for DNA or proteinshttps://biolib.com/bio-utils/clustalw/clustalw_biolibbiotools:clustalw_biolib2.1.Web applicationWeb APICommand-line toolBioinformatics portalhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0080Sequence analysisMacLinuxWindowsLGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1949nexus-seqhttp://edamontology.org/format_1997PHYLIP formatclustalw -INPUT=sequences.fasta -OUTFILE=alignment.fasta -OUTPUT=FASTAhttp://www.clustal.org/clustal2/General10.1093/bioinformatics/btm404WAREasy-to-use webserver that makes it possible to simultaneously use the best methods for aligning and predicting the consensus secondary structure for a set of non-coding RNA sequences.http://genome.ku.dk/resources/war/warbiotools:war1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1929FASTAhttp://genome.ku.dk/resources/war/pages/about.phpGeneral10.1093/nar/gkn275Primarybinf.ku.dkInstituteProviderStinus Lindgreenstinus@binf.ku.dkPersonPrimary contactMEME SuiteUnified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.http://meme-suite.org/meme_suitebiotools:meme_suiteCommand-line toolWeb applicationSuitehttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3125DNA binding siteshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_0238Sequence motif discoveryhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatMEME is a tool for discovering motifs in a group of related DNA or protein sequences. Note that MEME does not attempt to detect the alphabet from the sequences so you should specify it with the -dna or -protein options.http://edamontology.org/operation_0238Sequence motif discoveryhttp://edamontology.org/operation_0415Nucleic acid feature detectionhttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTMLMEME-ChIP performs several motif analysis steps on a set of DNA sequences that you provide. It is especially appropriate for analyzing the bound genomic regions identified in a transcription factor (TF) ChIP-seq experiment.MEME-ChIP can (1) discover novel DNA-binding motifs (with MEME and DREME), (2) determine which motifs are most centrally enriched (with CentriMo), (3) analyze them for similarity to known binding motifs (with Tomtom), and (4) automatically group the found motifs by similarity. A database of DNA motifs in MEME format. The immediate regions around individual ChIP-seq "peaks" from a transcription factor (TF) ChIP-seq experiment are ideal. MEME ChIP runs each program in its analysis in a different folder in the output directory. A summary file (index.html) is created in the output directory which lists the top motifs found and links to the results for each program.http://edamontology.org/operation_0238Sequence motif discoveryhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_1360meme-motifDREME (Discriminative Regular Expression Motif Elicitation) finds relatively short motifs (up to 8 bases) fast, and can perform discriminative motif discovery if given a negative set, consisting of sequences unlikely to contain a motif of interest that is however likely to be found in the main ("positive") sequence set. The sequences should all be approximately the same length. If these sequences are not supplied then the program will shuffle the positive sequences and use that set for the negative sequences. DREME writes an XML file to the output folder and converts it into a minimal MEME-formatted motif file and a human readable html file.http://edamontology.org/operation_0238Sequence motif discoveryhttp://edamontology.org/operation_0415Nucleic acid feature detectionhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatGLAM2 is a program for finding motifs in sequences, typically amino-acid or nucleotide sequences. The main innovation of GLAM2 is that it allows insertions and deletions in motifs. The Alphabet of the sequences. This can be 'p' for protein sequences, 'n' for nucleotide sequences or the name of an GLAM2 alphabet file. A file containing FASTA formatted sequences.http://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2070Sequence motif (nucleic acid)http://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_0951Statistical estimate scorehttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatAME (Analysis of Motif Enrichment) scores a set of DNA sequences given a set of DNA-binding motifs, treating each subsequence (and its reverse complement) in the sequence as a possible match to the motif. The sequences must be sorted by increasing value of some secondary criterion (e.g., expression level, peak height, fluorescence score). More than one file can be specified.http://edamontology.org/operation_0300Sequence profile alignmenthttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0869Sequence-profile alignmenthttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatCentriMo takes a set of motifs and a set of equal-length DNA or RNA sequences and plots the positional distribution of the best match of each motif. Ideally all of the same length. CentriMo outputs an HTML file that allows interactive selection of which motifs to plot the positional distribution for and control over smoothing and other plotting parameters.http://edamontology.org/operation_0445Transcription factor binding site predictionhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2070Sequence motif (nucleic acid)http://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_2070Sequence motif (nucleic acid)http://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2331HTMLSpaMo does inference of transcription factor complexes by looking for significant spacings between binding sites. This would typically be generated by expanding either side of a ChIP-seq peak to obtain sequences of about 500 bases in length. The primary motif is the motif for which you are trying to find cofactors. One or more MEME formatted motif files containing DNA motifs. The secondary motifs are tested for a significant spacing with the primary motif which might imply they act together.http://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/data_0582Ontologyhttp://edamontology.org/data_1772Scorehttp://edamontology.org/format_2332XMLhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2331HTMLThe name GOMO stands for "Gene Ontology for Motifs." The program searches in a set of ranked genes for enriched GO terms associated with high ranking genes. In other words, it identifies possible roles (Gene Ontology terms) for DNA binding motifs. A collection of GO terms mapped to to the sequences in the scoring file A XML file which contains for each motif the sequences and their score. By default GOMO calculates the ranksum statistics on the p-values of each gene given in the CisML input file.http://edamontology.org/operation_3438Calculationhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048ReportThe name FIMO stands for "Find Individual Motif Occurences." The program searches a database of DNA or protein sequences for occurrences of known motifs, treating each motif independently. See documentation for more details.http://edamontology.org/operation_0300Sequence profile alignmenthttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2331HTMLMAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs. MAST outputs three things: (1) The names of the high-scoring sequences sorted by the strength of the combined match of the sequence to all of the motifs in the group. (2) Motif diagrams showing the order and spacing of the motifs within each matching sequence. (3) Detailed annotation of each matching sequence showing the sequence and the locations and strengths of matches to the motifs.http://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048ReportMCAST searches a sequence database for statistically significant clusters of non-overlapping occurrences of a given set of motifs. See documentation for more details.http://edamontology.org/operation_0300Sequence profile alignmenthttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0857Sequence search resultsGLAM2SCAN finds matches, in a sequence database, to a motif discovered by GLAM2. Each match receives a score, indicating how well it fits the motif. The alphabet of the motif and sequences. This can be 'p' for protein sequences, 'n' for nucleotide sequences or the name of an GLAM2 alphabet file. A file containing a GLAM2 motif.http://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0300Sequence profile alignmenthttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatThe Tomtom program searches one or more query motifs against one or more databases of target motifs (and their DNA reverse complements), and reports for each query a list of target motifs, ranked by p-value. One or more files containing one or more motifs in MEME format.http://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_2305GFFThe name AMA stands for "Average Motif Affinity". The program scores a set of DNA sequences given a DNA-binding motif, treating each position in the sequence as a possible binding event. A file containing 0-order Markov Model in background model format such as produced by fasta-get-markov.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/format_3597psdhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert an BEEML matrix file into a MEME motif file suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifRead a CHEN matrix file and convert to MEME format. You may concatenate files for more than one motif.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1197InChIhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert an IUPAC motif into MEME motif format suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1367JASPAR formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert a directory of JASPAR files into a MEME motif suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert and merge multiple MEME formatted files into a single minimal meme format file.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert a nestedMICA (BioTiffin/XMS) matrix file into a MEME motif file suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert an PRIORITY matrix file into a MEME motif file suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert an RNA sequence to its binding motif in MEME motif format.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_1361Position frequency matrixhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert an SCPD matrix file into a MEME motif suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert a directory of files containing sites into a MEME motif file suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert a file containing the tab separated columns exported from the spreadsheet of Taipale results into MEME motif format. A Taipale file describes one or more motifs in terms of a probability matrix in column orientation.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert a TAMO file into a MEME motif file suitable for use with MEME Suite programs. A TAMO file describes one or more motifs in terms of a Log-odds matrix and a set of sites that were used to make the motif.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2082Matrixhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConvert a TRANSFAC 'matrix.dat' file into a MEME motif file suitable for use with MEME Suite programs.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2082Matrixhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifConverts UNIPROBE matricies from standard input into a MEME motif file suitable for use with MEME Suite programs. Can be several matricies.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAThis program converts a multiple alignment in clustalw format into a FASTA file.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1997PHYLIP formatThis program converts a multiple alignment in ClustalW format into a PHYLIP file.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0006Datahttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAThis program reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). Choose to output sequences in FASTA-with-gaps or MSF. The output format depends on input parameter.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0582Ontologyhttp://edamontology.org/format_2196OBO formathttp://edamontology.org/data_0582Ontologyhttp://edamontology.org/format_1915FormatConvert a Gene Ontology OBO file into a GO DAG file.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_2332XMLhttp://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_2330Textual formatProvides backwards compatibility by converting a mast xml file into a mast text file.http://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1966ASN.1 sequence formathttp://edamontology.org/format_1962strider formathttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1915Formathttp://edamontology.org/format_1925codatahttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1954Pearson formathttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1925codatahttp://edamontology.org/format_1962strider formathttp://edamontology.org/format_1915Formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1934fitch programhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1954Pearson formathttp://edamontology.org/format_1966ASN.1 sequence formatConverts protein and DNA sequence formats.http://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/data_2534Sequence attributehttp://edamontology.org/data_1022Sequence feature labelClassify a string passed as a command line argument as an instance of the DNA or protein alphabet. The letters of an unknown alphabet. The program prints 'DNA' or 'PROTEIN' to standard output, depending on the value of the alphabet argument.http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/data_0951Statistical estimate scoreRead an AMA output file and output each sequence name, p-value and q-value. For each sequence in the input, outputs the sequence name, the p-value of the sequence and the q-value (minimum false discovery rate).http://edamontology.org/operation_3480Probabilistic data generationhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3466EPShttp://edamontology.org/format_3604svgCreate motif logos. A file containing one or more motifs in MEME format. Logohttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_0006Datahttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/format_1915Formathttp://edamontology.org/data_0951Statistical estimate scorecompute-prior-dist computes the distribution of priors from a file in MEME PSP format. Number of increments to scale the distribution into. The first two lines are the minimum and maximum priors. Each succeeding line contains the probability that a prior is in the bin.http://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1940giFASTA formathttp://edamontology.org/data_1364Hidden Markov modelThe program fasta-get-markov estimates a Markov model from a FASTA file of sequences.http://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_3096Editinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTARead and write FASTA files.http://edamontology.org/operation_3429Generationhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTACreate a random subset of the sequences in a FASTA formatted file.http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_1772Scorehttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_1915Formatfitevd fits an extreme value distribution to a set of score-length pairs. Reads white-space separated score-length pairs from standard input.http://edamontology.org/operation_0230Sequence generationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAgendb generates the specified number of sequences using a Markov model.http://edamontology.org/operation_0236Sequence composition calculationhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1255Sequence featuresThe program getsize prints statistics about the FASTA sequences.http://edamontology.org/operation_0335Formattinghttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044SequenceThis program masks a glam2 motif out of sequences, so that weaker motifs can be found. The GLAM2 motif to mask with 'x' in the sequences. The FASTA formatted sequences to mask. The input sequences are output with the GLAM2 motif sites masked out with 'x's.http://edamontology.org/operation_0226Annotationhttp://edamontology.org/data_0582Ontologyhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2332XMLhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2332XMLUpdates the GOMO XML file(s) to add details about the GO terms, such as their name, hierarchy, relative position in that hierarchy and which are implied by others in the significant terms for each motif. A file containing the heirarchy of the GO terms in the format specified here. An XML file from GOMO to update. The GOMO XML File is updated to contain details about the GO terms heirarchy.http://edamontology.org/operation_0335Formattinghttp://edamontology.org/data_0006DataEasily rename MEME Suite HTML files to unique names incorporating the path name (rather than 'meme.html'). The program takes the names of one or more output directories created by MEME Suite programs such as MEME, CENTRIMO etc.http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1360meme-motifhttp://edamontology.org/data_1772ScoreThis utility calculates the statistical power of a phylogenetic motif model. Each line of the output has the following: Motif ID score score FPR False Positive Rate TPR True Positive Ratehttp://edamontology.org/operation_0238Sequence motif discoveryhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/format_2200FASTA-like (text)Generate position-specific priors from positive (likely to contain a feature of interest) and negative (unlikely to contain a feature of interest) sequences for use as an additional input to MEME. A file containing FASTA formatted sequences which are to be used as the primary set in PSP calculation. A file containing FASTA formatted sequences which are to be used as the control set in PSP calculation. A FASTA-like PSP format is written to standard output, it contains a prior for every position of every sequence in the primary set.http://edamontology.org/operation_0369Sequence cuttinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAPurge removes redundant sequences from a FASTA file. A file containing FASTA formatted sequences. This file will be overwritten. Purge overwrites the original FASTA sequence file with the purged sequences.http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_1669P-valuehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0951Statistical estimate scoreTakes as input a list of p-values and prints a corresponding list of q-values, computed using the method of Benjamini and Hochberg. A tab separated file containing a column of p-values. Other columns may exist Outputs tab-delimited columns.http://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formatGiven a tree and an alignment, identify the intersection of the sets of sequence IDs and leaf labels. Trim the extra sequences and leaves and print the resulting alignment and tree.http://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0863Sequence alignmentExtract specified range of columns from an alignment. The extracted region of the sequence alignment is written to standard output.http://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_1045Species namehttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0863Sequence alignmentRemove from an alignment all columns that contain a gap in the specified species. The name of a species present in the alignment for which gaps should be removed. The alignment, with the remaining columns that don't have gaps in the specified species, is written to standard output.http://edamontology.org/operation_0327Phylogenetic footprinting / shadowinghttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_2523Phylogenetic datahttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatPerform phylogenetic shadowing on a given DNA alignment, using a given tree. This program is a simplified version of motiph, in which the equilibrium distribution is set equal to the background model, rather than being taken from a given motif. This tree may contain additional species not represented in the alignment.http://meme-suite.org/doc/overview.html?man_type=webUser manual7584402758443988775008902357928375493664961684502810.1093/nar/gkp33519458158MEME Suite Supportmeme-suite@uw.eduPersonPrimary contactSPARSEVery efficient structure-based alignment of RNAs.http://www.bioinf.uni-freiburg.de/Software/SPARSEsparsebiotools:sparse1.8.9Command-line toolhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0080Sequence analysisLinuxMacPythonGPL-3.0de.NBIMatureFree of chargehttp://edamontology.org/operation_0294Structure-based sequence alignmenthttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_1465RNA structurehttp://edamontology.org/format_3466EPSA simultaneous alignment and folding tool with quadratic complexityhttp://www.bioinf.uni-freiburg.de/Software/SPARSE/General10.1093/bioinformatics/btv18525838465PMC4514930PrimaryMilad Miladimiladim@informatik.uni-freiburg.dehttp://orcid.org/0000-0002-0173-3009PersonDeveloperSebastian WillContributorUniversity FreiburgInstituteProviderrnateamInstituteProviderRolf Backofenrna@rna.informatik.uni-freiburg.dehttp://orcid.org/0000-0001-8231-3323DeveloperSebastian Willwill@bioinf.uni-leipzig.deDeveloperRolf Backofenrna@rna.informatik.uni-freiburg.dehttp://orcid.org/0000-0001-8231-3323PersonPrimary contactSebastian Willwill@bioinf.uni-leipzig.dePersonPrimary contactExpaRNA-PSimultaneous exact pattern matching and folding of RNAs.http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P/exparna-pbiotools:exparna-p1.8.9Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacGPL-3.0de.NBIMatureFree of chargehttp://edamontology.org/operation_0294Structure-based sequence alignmenthttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3466EPSExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. It computes the best arrangement of local sequence-structure (substructure) motifs common to two RNAs.http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P/General10.1186/s12859-014-0404-025551362PMC4302096PrimaryUniversity FreiburgInstituteProviderrnateamInstituteProviderRolf Backofenrna@rna.informatik.uni-freiburg.dehttp://orcid.org/0000-0001-8231-3323DeveloperChristina Ottoschmiedc@informatik.uni-freiburg.dePersonDeveloperRolf Backofenrna@rna.informatik.uni-freiburg.dehttp://orcid.org/0000-0001-8231-3323PersonPrimary contactChristina Ottoschmiedc@informatik.uni-freiburg.dePersonPrimary contactCARNA web serverAlignment of RNA structure ensembles.http://rna.informatik.uni-freiburg.de/CARNA/carnabiotools:carna1.2.5Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxWindowsMacde.NBIMatureFree of chargehttp://edamontology.org/operation_0294Structure-based sequence alignmenthttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3547Image formathttp://edamontology.org/format_3466EPShttp://edamontology.org/format_3508PDFhttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTACARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.http://rna.informatik.uni-freiburg.de/Help.jspGeneral10.1093/nar/gks49122689637PMC3394245PrimaryUniversity FreiburgInstituteProviderrnateamInstituteProviderRolf Backofenrna@rna.informatik.uni-freiburg.dehttp://orcid.org/0000-0001-8231-3323PersonDeveloperSebastian Willwill@bioinf.uni-leipzig.dePersonDeveloperRolf Backofenrna@rna.informatik.uni-freiburg.dehttp://orcid.org/0000-0001-8231-3323PersonPrimary contactSebastian Willwill@bioinf.uni-leipzig.dePersonPrimary contact