JalviewJalview 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_1476PDBOther 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/0000-0002-9014-5355trimAlTool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.https://trimal.readthedocs.iotrimalbiotools:trimal1.5.12.0-RCCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0160Sequence sites, features and motifsMacWindowsLinuxC++MatureFree of chargehttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_0863Sequence alignmenthttps://github.com/inab/trimalRepositoryhttps://github.com/inab/trimalSource code1.5.1https://github.com/inab/trimal/tree/2.0_RCSource code2.0-RChttp://trimal.cgenomics.org/GeneralOld versionshttps://trimal.readthedocs.ioGeneral10.1093/bioinformatics/btp34819505945PMC2712344Salvador Capella-Gutierrezsalcagu@gmail.comPersonPrimary contacttgabaldon@crg.eshttp://gabaldonlab.crg.es/PersonPrimary contactmsaDisplay multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.http://msa.biojs.netmsabiotools:msa1.0.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacJavaScriptApache-2.0Rostlab toolsBioconductorBioJSMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1984FASTA-alnVisualizes 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 formathttps://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 contactWAREasy-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://genome.ku.dk/resources/war/pages/about.phpGeneral10.1093/nar/gkn27518492721PMC2447782Primarybinf.ku.dkInstituteProviderStinus Lindgreenstinus@binf.ku.dkPersonPrimary contactClustalW (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_1929FASTAclustalw -INPUT=sequences.fasta -OUTFILE=alignment.fasta -OUTPUT=FASTAhttp://www.clustal.org/clustal2/General10.1093/bioinformatics/btm40417846036MUSCLEThis 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 formathttps://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.1114334.1Primary510.1186/1471-2105-5-11315318951PMC517706Other10.1101/2021.06.20.449169Primary5Alex 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 contactDeveloperkc-alignA fast and accurate tool for performing codon-aware multiple sequence alignments.
Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment.
Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout.https://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_1929FASTAkc-align -m genome -r reference.fasta -S sequences.fasta -s 3532,3892 -e 3894,5326https://github.com/davebx/kc-align/blob/dev/README.mdGeneralMEME 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_1929FASTAMEME 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_1929FASTAMEME-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_1929FASTADREME (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 setGLAM2 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-motifAME (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_1929FASTACentriMo 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-motifSpaMo 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_2332XMLThe 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_1929FASTAThe 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_1929FASTAMAST 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_1929FASTAMCAST 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_1929FASTAGLAM2SCAN 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-motifThe 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 modelThe 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_3597psdConvert 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 matrixRead 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_1197InChIConvert 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 formatConvert 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-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 matrixConvert 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_1915FormatConvert 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_1929FASTAConvert 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_1915FormatConvert 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 formatConvert 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_3752CSVConvert 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_1915FormatConvert 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_1915FormatConvert 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_1915FormatConverts 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 formatThis 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 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_1915FormatThis 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 formatConvert a Gene Ontology OBO file into a GO DAG file.http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_2332XMLProvides 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 formatConverts protein and DNA sequence formats.http://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/data_2534Sequence attributeClassify 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 trackRead 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-motifCreate 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_1915Formatcompute-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 formatThe 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_1929FASTARead and write FASTA files.http://edamontology.org/operation_3429Generationhttp://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_1772Scorefitevd 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 generationgendb 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_1929FASTAThe 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_1929FASTAThis 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_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-motifThis 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_1929FASTAGenerate 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_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 formatTakes 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 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 formatExtract 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 formatRemove 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 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_1929FASTAA 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_1929FASTAExpaRNA 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_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 contactLocARNA-PProbabilistic structure-based multiple alignment of RNAs.http://www.bioinf.uni-freiburg.de/Software/LocARNA/locarna-pbiotools:locarna-p1.8.9Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacC++de.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_1929FASTALocARNA simultaneously folds and aligns input sequences. Specifications of additional constraints or fixed input structures are possible.http://www.bioinf.uni-freiburg.de/Software/LocARNA/General10.1261/rna.029041.11122450757PMC3334699PrimaryUniversity 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 contactLocARNAStructure-based multiple alignment of RNAs.http://www.bioinf.uni-freiburg.de/Software/LocARNA/locarnabiotools:locarna1.8.9Command-line toolhttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacC++GPL-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_1929FASTALocARNA simultaneously folds and aligns input sequences. Specifications of additional constraints or fixed input structures are possible.https://github.com/s-will/LocARNA/blob/master/READMEGeneral10.1371/journal.pcbi.003006517432929PMC1851984PrimaryUniversity FreiburgInstituteProviderRNA tools and software consortiumConsortiumDocumentorRolf 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