count: 13
list:
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview 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.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Format
        uri: http://edamontology.org/format_1915
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: Format
        uri: http://edamontology.org/format_1915
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-04T13:26:28.643607Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://source.jalview.org/crucible/browse/jalview
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata:
      abstract: ''
      authors: []
      citationCount: 7499
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
  - biotoolsID: jabaws
    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
    type: uses
  - biotoolsID: ensembl
    type: uses
  - biotoolsID: pdb
    type: uses
  - biotoolsID: rfam
    type: uses
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.5.0
- accessibility: null
  additionDate: '2016-06-02T02:47:10Z'
  biotoolsCURIE: biotools:msa
  biotoolsID: msa
  collectionID:
  - Rostlab tools
  - Bioconductor
  - BioJS
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Wilzbach
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ian Sillitoe
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Guy Yachdav
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Benedikt Rauscher
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tatyana Goldberg
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Technische Universität München
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Google Summer of Code (GSoC) 2014
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: BioJS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://github.com/wilzbach/msa
  - email: bodenhofer@bioinf.jku.at
    fundrefid: null
    gridid: null
    name: Ulrich Bodenhofer
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Display 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.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://github.com/wilzbach/msa/blob/master/LICENSE
  - note: null
    type:
    - General
    url: http://msa.biojs.net
  download:
  - note: null
    type: Source code
    url: https://github.com/wilzbach/msa
    version: null
  - note: null
    type: Binaries
    url: https://cdn.bio.sh/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    note: 'Visualizes multiple sequence alignment, calculates conservation, shows
      sequence logo, applies multiple color schemes A multiple sequence alignment
      (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment
      Images are exported in PNG Export sequences in FASTA format Export features
      in GFF

      NOTE: Actually, all these output types of data should instead be under separate
      "constant" operations, while the visualisation should be an unary operation,
      perhaps without an output.'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Sequence alignment image
        uri: http://edamontology.org/data_1711
      format:
      - term: Image format
        uri: http://edamontology.org/format_3547
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment report
        uri: http://edamontology.org/data_0867
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: http://msa.biojs.net
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2024-11-25T16:17:03.898741Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/wilzbach/msa
  - note: null
    type:
    - Software catalogue
    url: http://biojs.io/
  - note: null
    type:
    - Helpdesk
    url: http://github.com/wilzbach/msa
  - note: null
    type:
    - Mirror
    url: http://www.bioinf.jku.at/software/msa/
  maturity: Mature
  name: msa
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioJS
  publication:
  - doi: 10.1093/bioinformatics/btw474
    metadata: null
    note: null
    pmcid: PMC5181560
    pmid: '27412096'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btv494
    metadata: null
    note: null
    pmcid: null
    pmid: '26315911'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2015-07-28T11:14:46Z'
  biotoolsCURIE: biotools:war
  biotoolsID: war
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: binf.ku.dk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: stinus@binf.ku.dk
    fundrefid: null
    gridid: null
    name: Stinus Lindgreen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Easy-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.
  documentation:
  - note: null
    type:
    - General
    url: http://genome.ku.dk/resources/war/pages/about.php
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
    note: null
    operation:
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: http://genome.ku.dk/resources/war/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:06:15.464725Z'
  license: null
  link: []
  maturity: null
  name: WAR
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1093/nar/gkn275
    metadata:
      abstract: 'We present an easy-to-use webserver that makes it possible to simultaneously
        use a number of state of the art methods for performing multiple alignment
        and secondary structure prediction for noncoding RNA sequences. This makes
        it possible to use the programs without having to download the code and get
        the programs to run. The results of all the programs are presented on a webpage
        and can easily be downloaded for further analysis. Additional measures are
        calculated for each program to make it easier to judge the individual predictions,
        and a consensus prediction taking all the programs into account is also calculated.
        This website is free and open to all users and there is no login requirement.
        The webserver can be found at: http://genome.ku.dk/resources/war.'
      authors:
      - name: Torarinsson E.
      - name: Lindgreen S.
      citationCount: 41
      date: '2008-01-01T00:00:00Z'
      journal: Nucleic acids research
      title: 'WAR: Webserver for aligning structural RNAs.'
    note: null
    pmcid: PMC2447782
    pmid: '18492721'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2021-10-22T10:16:40.495992Z'
  biotoolsCURIE: biotools:clustalw_biolib
  biotoolsID: clustalw_biolib
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: ClustalW is a general purpose multiple sequence alignment program for
    DNA or proteins
  documentation:
  - note: null
    type:
    - General
    url: http://www.clustal.org/clustal2/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: clustalw -INPUT=sequences.fasta -OUTFILE=alignment.fasta -OUTPUT=FASTA
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: nexus-seq
        uri: http://edamontology.org/format_1949
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
  homepage: https://biolib.com/bio-utils/clustalw/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T20:17:36.321599Z'
  license: LGPL-3.0
  link: []
  maturity: Mature
  name: ClustalW (BioLib)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: laurasansc
  publication:
  - doi: 10.1093/bioinformatics/btm404
    metadata:
      abstract: 'Summary: The Clustal W and Clustal X multiple sequence alignment
        programs have been completely rewritten in C++. This will facilitate the further
        development of the alignment algorithms in the future and has allowed proper
        porting of the programs to the latest versions of Linux, Macintosh and Windows
        operating systems. © The Author 2007. Published by Oxford University Press.
        All rights reserved.'
      authors:
      - name: Larkin M.A.
      - name: Blackshields G.
      - name: Brown N.P.
      - name: Chenna R.
      - name: Mcgettigan P.A.
      - name: McWilliam H.
      - name: Valentin F.
      - name: Wallace I.M.
      - name: Wilm A.
      - name: Lopez R.
      - name: Thompson J.D.
      - name: Gibson T.J.
      - name: Higgins D.G.
      citationCount: 24337
      date: '2007-11-01T00:00:00Z'
      journal: Bioinformatics
      title: Clustal W and Clustal X version 2.0
    note: null
    pmcid: null
    pmid: '17846036'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Web API
  - Command-line tool
  - Bioinformatics portal
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 2.1.
- accessibility: Open access
  additionDate: '2017-01-17T14:57:39Z'
  biotoolsCURIE: biotools:muscle
  biotoolsID: muscle
  collectionID:
  - MUSCLE
  - galaxyPasteur
  - BioConductor
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: alex.t.kalinka@gmail.com
    fundrefid: null
    gridid: null
    name: Alex T. Kalinka
    note: Maintainer of the BioConductor package
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: EBI Web Service support
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.ebi.ac.uk/support/
  - email: null
    fundrefid: null
    gridid: null
    name: Technical Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.drive5.com/muscle/manual/support.html
  - email: robert@drive5.com
    fundrefid: null
    gridid: null
    name: Robert Edgar
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: This tool performs multiple sequence alignments of nucleotide or amino
    acid sequences.
  documentation:
  - note: BioConductor package documentation
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/muscle.html
  - note: EBI Web Service documentation
    type:
    - API documentation
    url: https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_rest
  - note: null
    type:
    - User manual
    url: https://www.drive5.com/muscle/manual/
  - note: null
    type:
    - Installation instructions
    url: https://www.drive5.com/muscle/manual/install.html
  download:
  - note: BioConductor package
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/muscle_3.16.0.tar.gz
    version: null
  - note: EBI MUSCLE Web Service
    type: API specification
    url: https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_rest
    version: null
  - note: null
    type: Downloads page
    url: https://www.drive5.com/muscle/downloads.htm
    version: null
  editPermission:
    authors:
    - laurasansc
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://www.drive5.com/muscle/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T20:10:00.504033Z'
  license: Other
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.biocatalogue.org/services/3135
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/muscle/3.8.31.1
  maturity: Mature
  name: MUSCLE
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bioconductor_import
  publication:
  - doi: 10.1093/nar/gkh340
    metadata:
      abstract: 'We describe MUSCLE, a new computer program for creating multiple
        alignments of protein sequences. Elements of the algorithm include fast distance
        estimation using kmer counting, progressive alignment using a new profile
        function we call the log-expectation score, and refinement using tree-dependent
        restricted partitioning. The speed and accuracy of MUSCLE are compared with
        T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE,
        SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or
        joint highest, rank in accuracy on each of these sets. Without refinement,
        MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee
        and MAFFT, and is the fastest of the tested methods for large numbers of sequences,
        aligning 5000 sequences of average length 350 in 7 min on a current desktop
        computer. The MUSCLE program, source code and PREFAB test data are freely
        available at http://www.drive5.com/muscle. © Oxford University Press 20004;
        all rights reserved.'
      authors:
      - name: Edgar R.C.
      citationCount: 34929
      date: '2004-07-09T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MUSCLE: Multiple sequence alignment with high accuracy and high throughput'
    note: null
    pmcid: PMC390337
    pmid: '15034147'
    type:
    - Primary
    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '5'
  - doi: 10.1186/1471-2105-5-113
    metadata:
      abstract: 'Background: In a previous paper, we introduced MUSCLE, a new program
        for creating multiple alignments of protein sequences, giving a brief summary
        of the algorithm and showing MUSCLE to achieve the highest scores reported
        to date on four alignment accuracy benchmarks. Here we present a more complete
        discussion of the algorithm, describing several previously unpublished techniques
        that improve biological accuracy and / or computational complexity. We introduce
        a new option, MUSCLE-fast, designed for high-throughput applications. We also
        describe a new protocol for evaluating objective functions that align two
        profiles. Results: We compare the speed and accuracy of MUSCLE with CLUSTALW,
        Progressive POA and the MAFFT script FFTNS1, the fastest previously published
        program known to the author. Accuracy is measured using four benchmarks: BAliBASE,
        PREFAB, SABmark and SMART. We test three variants that offer highest accuracy
        (MUSCLE with default settings), highest speed (MUSCLEfast), and a carefully
        chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be
        the fastest algorithm on all test sets, achieving average alignment accuracy
        similar to CLUSTALW in times that are typically two to three orders of magnitude
        less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in
        21 seconds on a current desktop computer. Conclusions: MUSCLE offers a range
        of options that provide improved speed and / or alignment accuracy compared
        with currently available programs. MUSCLE is freely available at http:// www.drive5.com/muscle.
        © 2004 Edgar; licensee BioMed Central Ltd.'
      authors:
      - name: Edgar R.C.
      citationCount: 6857
      date: '2004-08-19T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'MUSCLE: A multiple sequence alignment method with reduced time and space
        complexity'
    note: null
    pmcid: PMC517706
    pmid: '15318951'
    type:
    - Other
    version: null
  - doi: 10.1101/2021.06.20.449169
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '5'
  relation: []
  toolType:
  - Command-line tool
  - Web API
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '5'
- accessibility: null
  additionDate: '2017-04-15T08:42:53Z'
  biotoolsCURIE: biotools:trimal
  biotoolsID: trimal
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: salcagu@gmail.com
    fundrefid: null
    gridid: null
    name: Salvador Capella-Gutierrez
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: tgabaldon@crg.es
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://gabaldonlab.crg.es/
  description: Tool for the automated removal of spurious sequences or poorly aligned
    regions from a multiple sequence alignment.
  documentation:
  - note: Old versions
    type:
    - General
    url: http://trimal.cgenomics.org/
  - note: null
    type:
    - General
    url: https://trimal.readthedocs.io
  download:
  - note: null
    type: Source code
    url: https://github.com/inab/trimal
    version: 1.5.0
  - note: null
    type: Source code
    url: https://github.com/inab/trimal/tree/2.0_RC
    version: 2.0-RC
  editPermission:
    authors:
    - nico_bsc
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: phylipnon
        uri: http://edamontology.org/format_1998
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://trimal.readthedocs.io
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-24T13:51:16.771755Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/inab/trimal
  maturity: Mature
  name: trimAl
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: scapella
  publication:
  - doi: 10.1093/bioinformatics/btp348
    metadata:
      abstract: Multiple sequence alignments are central to many areas of bioinformatics.
        It has been shown that the removal of poorly aligned regions from an alignment
        increases the quality of subsequent analyses. Such an alignment trimming phase
        is complicated in large-scale phylogenetic analyses that deal with thousands
        of alignments. Here, we present trimAl, a tool for automated alignment trimming,
        which is especially suited for large-scale phylogenetic analyses. trimAl can
        consider several parameters, alone or in multiple combinations, for selecting
        the most reliable positions in the alignment. These include the proportion
        of sequences with a gap, the level of amino acid similarity and, if several
        alignments for the same set of sequences are provided, the level of consistency
        across different alignments. Moreover, trimAl can automatically select the
        parameters to be used in each specific alignment so that the signal-to-noise
        ratio is optimized. © 2009 The Author(s).
      authors:
      - name: Capella-Gutierrez S.
      - name: Silla-Martinez J.M.
      - name: Gabaldon T.
      citationCount: 6971
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'trimAl: A tool for automated alignment trimming in large-scale phylogenetic
        analyses'
    note: null
    pmcid: PMC2712344
    pmid: '19505945'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - 1.5.0
  - 2.0-RC
- accessibility: Open access
  additionDate: '2022-06-24T09:15:31.387295Z'
  biotoolsCURIE: biotools:kc-align
  biotoolsID: kc-align
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: "A fast and accurate tool for performing codon-aware multiple sequence\
    \ alignments. \n\nKc-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.\n\nKc-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."
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/davebx/kc-align/blob/dev/README.md
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: kc-align -m genome -r reference.fasta -S sequences.fasta -s 3532,3892 -e
      3894,5326
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/davebx/kc-align
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-07T08:41:36.745350Z'
  license: AFL-3.0
  link: []
  maturity: null
  name: kc-align
  operatingSystem: []
  otherID: []
  owner: m.bernt
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2017-02-10T14:15:59Z'
  biotoolsCURIE: biotools:meme_suite
  biotoolsID: meme_suite
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: meme-suite@uw.edu
    fundrefid: null
    gridid: null
    name: MEME Suite Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Unified 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.
  documentation:
  - note: null
    type:
    - User manual
    url: http://meme-suite.org/doc/overview.html?man_type=web
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: MEME 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.
    operation:
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: MEME-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.
    operation:
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    - term: Protein binding site prediction
      uri: http://edamontology.org/operation_2575
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: DREME (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.
    operation:
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format: []
    note: GLAM2 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.
    operation:
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence motif (nucleic acid)
        uri: http://edamontology.org/data_2070
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    note: AME (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.
    operation:
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: CentriMo 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.
    operation:
    - term: Sequence profile alignment
      uri: http://edamontology.org/operation_0300
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Sequence-profile alignment
        uri: http://edamontology.org/data_0869
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence motif (nucleic acid)
        uri: http://edamontology.org/data_2070
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence motif (nucleic acid)
        uri: http://edamontology.org/data_2070
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    note: SpaMo 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.
    operation:
    - term: Transcription factor binding site prediction
      uri: http://edamontology.org/operation_0445
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Ontology
        uri: http://edamontology.org/data_0582
      format: []
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    note: The 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.
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: The 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.
    operation:
    - term: Calculation
      uri: http://edamontology.org/operation_3438
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: 'MAST 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.'
    operation:
    - term: Sequence profile alignment
      uri: http://edamontology.org/operation_0300
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: MCAST searches a sequence database for statistically significant clusters
      of non-overlapping occurrences of a given set of motifs. See documentation for
      more details.
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format: []
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: GLAM2SCAN 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.
    operation:
    - term: Sequence profile alignment
      uri: http://edamontology.org/operation_0300
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    note: The 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.
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Sequence profile alignment
      uri: http://edamontology.org/operation_0300
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format: []
    note: The 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.
    operation:
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: Protein binding site prediction
      uri: http://edamontology.org/operation_2575
    output:
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
  - cmd: null
    input:
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format:
      - term: psd
        uri: http://edamontology.org/format_3597
    note: Convert an BEEML matrix file into a MEME motif file suitable for use with
      MEME Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format: []
    note: Read a CHEN matrix file and convert to MEME format. You may concatenate
      files for more than one motif.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: InChI
        uri: http://edamontology.org/format_1197
    note: Convert an IUPAC motif into MEME motif format suitable for use with MEME
      Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: JASPAR format
        uri: http://edamontology.org/format_1367
    note: Convert a directory of JASPAR files into a MEME motif suitable for use with
      MEME Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    note: Convert and merge multiple MEME formatted files into a single minimal meme
      format file.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format: []
    note: Convert a nestedMICA (BioTiffin/XMS) matrix file into a MEME motif file
      suitable for use with MEME Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: Convert an PRIORITY matrix file into a MEME motif file suitable for use
      with MEME Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Convert an RNA sequence to its binding motif in MEME motif format.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Position frequency matrix
        uri: http://edamontology.org/data_1361
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: Convert an SCPD matrix file into a MEME motif suitable for use with MEME
      Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: Convert a directory of files containing sites into a MEME motif file suitable
      for use with MEME Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: Convert 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.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: Convert 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.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: Convert a TRANSFAC 'matrix.dat' file into a MEME motif file suitable for
      use with MEME Suite programs.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: Converts UNIPROBE matricies from standard input into a MEME motif file suitable
      for use with MEME Suite programs. Can be several matricies.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: This program converts a multiple alignment in clustalw format into a FASTA
      file.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: This program converts a multiple alignment in ClustalW format into a PHYLIP
      file.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format: []
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: This 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.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Ontology
        uri: http://edamontology.org/data_0582
      format:
      - term: OBO format
        uri: http://edamontology.org/format_2196
    note: Convert a Gene Ontology OBO file into a GO DAG file.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Ontology
        uri: http://edamontology.org/data_0582
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
  - cmd: null
    input:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    note: Provides backwards compatibility by converting a mast xml file into a mast
      text file.
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: ASN.1 sequence format
        uri: http://edamontology.org/format_1966
      - term: strider format
        uri: http://edamontology.org/format_1962
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: codata
        uri: http://edamontology.org/format_1925
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: Pearson format
        uri: http://edamontology.org/format_1954
      - term: Nexus format
        uri: http://edamontology.org/format_1912
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: Converts protein and DNA sequence formats.
    operation:
    - term: Sequence conversion
      uri: http://edamontology.org/operation_0233
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: codata
        uri: http://edamontology.org/format_1925
      - term: strider format
        uri: http://edamontology.org/format_1962
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: fitch program
        uri: http://edamontology.org/format_1934
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: Nexus format
        uri: http://edamontology.org/format_1912
      - term: Pearson format
        uri: http://edamontology.org/format_1954
      - term: ASN.1 sequence format
        uri: http://edamontology.org/format_1966
  - cmd: null
    input:
    - data:
        term: Sequence attribute
        uri: http://edamontology.org/data_2534
      format: []
    note: Classify 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.
    operation:
    - term: Sequence classification
      uri: http://edamontology.org/operation_2995
    output:
    - data:
        term: Sequence feature label
        uri: http://edamontology.org/data_1022
      format: []
  - cmd: null
    input:
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format: []
    note: Read 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).
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    note: Create motif logos. A file containing one or more motifs in MEME format.
      Logo
    operation:
    - term: Probabilistic data generation
      uri: http://edamontology.org/operation_3480
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: svg
        uri: http://edamontology.org/format_3604
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format: []
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
    note: compute-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.
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: giFASTA format
        uri: http://edamontology.org/format_1940
    note: The program fasta-get-markov estimates a Markov model from a FASTA file
      of sequences.
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Read and write FASTA files.
    operation:
    - term: Loading
      uri: http://edamontology.org/operation_1812
    - term: Editing
      uri: http://edamontology.org/operation_3096
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Create a random subset of the sequences in a FASTA formatted file.
    operation:
    - term: Generation
      uri: http://edamontology.org/operation_3429
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    note: fitevd fits an extreme value distribution to a set of score-length pairs.
      Reads white-space separated score-length pairs from standard input.
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
  - cmd: null
    input: []
    note: gendb generates the specified number of sequences using a Markov model.
    operation:
    - term: Sequence generation
      uri: http://edamontology.org/operation_0230
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: The program getsize prints statistics about the FASTA sequences.
    operation:
    - term: Sequence composition calculation
      uri: http://edamontology.org/operation_0236
    output:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format: []
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: This 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.
    operation:
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
  - cmd: null
    input:
    - data:
        term: Ontology
        uri: http://edamontology.org/data_0582
      format: []
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    note: Updates 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.
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format: []
    note: Easily 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.
    operation:
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output: []
  - cmd: null
    input:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: meme-motif
        uri: http://edamontology.org/format_1360
    note: 'This 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 Rate'
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: 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.
    operation:
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    output:
    - data:
        term: Position-specific scoring matrix
        uri: http://edamontology.org/data_2854
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Purge 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.
    operation:
    - term: Sequence cutting
      uri: http://edamontology.org/operation_0369
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: P-value
        uri: http://edamontology.org/data_1669
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: Takes 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.
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format: []
  - cmd: null
    input:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: Given 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.
    operation:
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: Extract specified range of columns from an alignment. The extracted region
      of the sequence alignment is written to standard output.
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  - cmd: null
    input:
    - data:
        term: Species name
        uri: http://edamontology.org/data_1045
      format: []
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: Remove 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.
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  - cmd: null
    input:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: Perform 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.
    operation:
    - term: Phylogenetic footprinting / shadowing
      uri: http://edamontology.org/operation_0327
    output:
    - data:
        term: Phylogenetic data
        uri: http://edamontology.org/data_2523
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://meme-suite.org/
  homepage_status: 0
  language: []
  lastUpdate: '2019-02-04T13:59:48Z'
  license: null
  link: []
  maturity: null
  name: MEME Suite
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: null
    metadata:
      abstract: The algorithm described in this paper discovers one or more motifs
        in a collection of DNA or protein sequences by using the technique of expectation
        maximization to fit a two-component finite mixture model to the set of sequences.
        Multiple motifs are found by fitting a mixture model to the data, probabilistically
        erasing the occurrences of the motif thus found, and repeating the process
        to find successive motifs. The algorithm requires only a set of unaligned
        sequences and a number specifying the width of the motifs as input. It returns
        a model of each motif and a threshold which together can be used as a Bayes-optimal
        classifier for searching for occurrences of the motif in other databases.
        The algorithm estimates how many times each motif occurs in each sequence
        in the dataset and outputs an alignment of the occurrences of the motif. The
        algorithm is capable of discovering several different motifs with differing
        numbers of occurrences in a single dataset.
      authors:
      - name: Bailey T.L.
      - name: Elkan C.
      citationCount: 3490
      date: '1994-01-01T00:00:00Z'
      journal: Proceedings / ... International Conference on Intelligent Systems for
        Molecular Biology ; ISMB. International Conference on Intelligent Systems
        for Molecular Biology
      title: Fitting a mixture model by expectation maximization to discover motifs
        in biopolymers.
    note: null
    pmcid: null
    pmid: '7584402'
    type: []
    version: null
  - doi: null
    metadata:
      abstract: MEME is a tool for discovering motifs in sets of protein or DNA sequences.
        This paper describes several extensions to MEME which increase its ability
        to find motifs in a totally unsupervised fashion, but which also allow it
        to benefit when prior knowledge is available. When no background knowledge
        is asserted. MEME obtains increased robustness from a method for determining
        motif widths automatically, and from probabilistic models that allow motifs
        to be absent in some input sequences. On the other hand, MEME can exploit
        prior knowledge about a motif being present in all input sequences, about
        the length of a motif and whether it is a palindrome, and (using Dirichlet
        mixtures) about expected patterns in individual motif positions. Extensive
        experiments are reported which support the claim that MEME benefits from,
        but does not require, background knowledge. The experiments use seven previously
        studied DNA and protein sequence families and 75 of the protein families documented
        in the Prosite database of sites and patterns, Release 11.1.
      authors:
      - name: Bailey T.L.
      - name: Elkan C.
      citationCount: 531
      date: '1995-01-01T00:00:00Z'
      journal: Proceedings / ... International Conference on Intelligent Systems for
        Molecular Biology ; ISMB. International Conference on Intelligent Systems
        for Molecular Biology
      title: The value of prior knowledge in discovering motifs with MEME.
    note: null
    pmcid: null
    pmid: '7584439'
    type: []
    version: null
  - doi: null
    metadata:
      abstract: Several computer algorithms for discovering patterns in groups of
        protein sequences are in use that are based on fitting the parameters of a
        statistical model to a group of related sequences. These include hidden Markov
        model (HMM) algorithms for multiple sequence alignment, and the MEME and Gibbs
        sampler algorithms for discovering motifs. These algorithms are sometimes
        prone to producing models that are incorrect because two or more patients
        have been combined. The statistical model produced in this situation is a
        convex combination (weighted average) of two or more different models. This
        paper presents a solution to the problem of convex combinations in the form
        of a heuristic based on using extremely low variance Dirichlet mixture priors
        as part of the statistical model. This heuristic, which we call the megaprior
        heuristic, increase the strength (i.e., decreases the variance) of the prior
        in proportion to the size of the sequence dataset. This causes each column
        in the final model to strongly resemble the mean of a single component of
        the prior, regardless of the size of the dataset. We describe the cause of
        the convex combination problem, analyze it mathematically, motivate and describe
        the implementation of the megaprior heuristic, and show how it can effectively
        eliminate the problem of convex combinations in protein sequence pattern discovery.
      authors:
      - name: Bailey T.L.
      - name: Gribskov M.
      citationCount: 25
      date: '1996-01-01T00:00:00Z'
      journal: Proceedings / ... International Conference on Intelligent Systems for
        Molecular Biology ; ISMB. International Conference on Intelligent Systems
        for Molecular Biology
      title: The megaprior heuristic for discovering protein sequence patterns.
    note: null
    pmcid: null
    pmid: '8877500'
    type: []
    version: null
  - doi: null
    metadata:
      abstract: Many advanced software tools fail to reach a wide audience because
        they require specialized hardware, installation expertise, or an abundance
        of CPU cycles. The worldwide web offers a new opportunity for distributing
        such systems. One such program, MEME, discovers repeated patterns, called
        motifs, in sets of DNA or protein sequences. This tool is now available to
        biologists over the worldwide web, using an asynchronous, single-program multiple-data
        version of the program called ParaMEME that runs on an Intel Paragon XP/S
        parallel computer at the San Diego Super-computer Center. ParaMEME scales
        gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data
        sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively
        from a user, submits the sequences to the Paragon for analysis, and e-mails
        the results back to the user. ParaMEME is available for free public use at
        http://www. sdsc. edu/CompSci/Biomed/ MEME. © 1996, Oxford University Press.
      authors:
      - name: Grundy W.N.
      - name: Bailey T.L.
      - name: Eikan C.P.
      citationCount: 73
      date: '1996-01-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Parameme: A parallel implementation and a web interface for a dna and
        protein motif discovery tool'
    note: null
    pmcid: null
    pmid: '8902357'
    type: []
    version: null
  - doi: null
    metadata:
      abstract: 'Motivation: Modeling families of related biological sequences using
        Hidden Markov models (HMMs), although increasingly widespread, faces at least
        one major problem: because of the complexity of these mathematical models,
        they require a relatively large training set in order to accurately recognize
        a given family. For families in which there are few known sequences, a standard
        linear HMM contains too many parameters to be trained adequately Results:
        This work attempts to solve that problem by generating smaller HMMs which
        precisely model only the conserved regions of the family. These HMMs are constructed
        from motif models generated by the EM algorithm using the MEME software. Because
        motif-based HMMs have relatively few parameters, they can be trained using
        smaller data sets. Studies of short chain alcohol dehydrogenases and 4Fe-4S
        ferredoxins support the claim that motif-based HMMs exhibit increased sensitivity
        and selectivity in database searches, especially when training sets contain
        few sequences. Availability: http://www.sdsc.edu/MEME Contact: bgrundy@cs.ucsd.edu.
        © 1997, Oxford University Press.'
      authors:
      - name: Grundy W.N.
      - name: Bailey T.L.
      - name: Baker M.E.
      - name: Eikan C.P.
      citationCount: 154
      date: '1997-01-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Meta-meme: Motif-based hidden markov models of protein families'
    note: null
    pmcid: null
    pmid: '9283754'
    type: []
    version: null
  - doi: null
    metadata:
      abstract: 'MEME (Multiple Expectation-maximization for Motif Elicitation) is
        a unique new software tool that uses artificial intelligence techniques to
        discover motifs shared by a set of protein sequences in a fully automated
        manner. This paper is the first detailed study of the use of MEME to analyse
        a large, biologically relevant set of sequences, and to evaluate the sensitivity
        and accuracy of MEME in identifying structurally important motifs. For this
        purpose, we chose the short-chain alcohol dehydrogenase superfamily because
        it is large and phylogenetically diverse, providing a test of how well MEME
        can work on sequences with low amino acid similarity. Moreover, this dataset
        contains enzymes of biological importance, and because several enzymes have
        known X-ray crystallographic structures, we can test the usefulness of MEME
        for structural analysis. The first six motifs from MEME map onto structurally
        important cl-helices and β-strands on Streptomyces hydrogenans 20β-hydroxysteroid
        dehydrogenase. We also describe MAST (Motif Alignment Search Tool), which
        conveniently uses output: from MEME for searching databases such as SWISS-PROT
        and Genpept. MAST provides statistical measures that hermit a rigorous evaluation
        of the significance of database searches with individual motifs or groups
        of motifs. A database search of Genpept90 by MAST with the log-odds matrix
        of the first six motifs obtained from MEME yields a bimodal output, demonstrating.
        the selectivity of MAST. We show for the first time, using primary sequence
        analysis, that bacterial sugar epimerases are homologs of short-chain dehydrogenases.
        MEME and MAST will be increasingly useful as genome sequencing provides large
        datasets of phylogenetically divergent sequences of biomedical interest.'
      authors:
      - name: Bailey T.L.
      - name: Baker M.E.
      - name: Elkan C.P.
      citationCount: 55
      date: '1997-05-01T00:00:00Z'
      journal: Journal of Steroid Biochemistry and Molecular Biology
      title: 'An artificial intelligence approach to motif discovery in protein sequences:
        Application to steroid dehydrogenases'
    note: null
    pmcid: null
    pmid: '9366496'
    type: []
    version: null
  - doi: null
    metadata:
      abstract: MEME (Multiple EM for Motif Elicitation) is one of the most widely
        used tools for searching for novel 'signals' in sets of biological sequences.
        Applications include the discovery of new transcription factor binding sites
        and protein domains. MEME works by searching for repeated, ungapped sequence
        patterns that occur in the DNA or protein sequences provided by the user.
        Users can perform MEME searches via the web server hosted by the National
        Biomedical Computation Resource (http://meme. nbcr.net) and several mirror
        sites. Through the same web server, users can also access the Motif Alignment
        and Search Tool to search sequence databases for matches to motifs encoded
        in several popular formats. By clicking on buttons in the MEME output, users
        can compare the motifs discovered in their input sequences with databases
        of known motifs, search sequence databases for matches to the motifs and display
        the motifs in various formats. This article describes the freely accessible
        web server and its architecture, and discusses ways to use MEME effectively
        to find new sequence patterns in biological sequences and analyze their significance.
        © The Author 2006. Published by Oxford University Press. All rights reserved.
      authors:
      - name: Bailey T.L.
      - name: Williams N.
      - name: Misleh C.
      - name: Li W.W.
      citationCount: 1542
      date: '2006-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MEME: Discovering and analyzing DNA and protein sequence motifs'
    note: null
    pmcid: null
    pmid: '16845028'
    type: []
    version: null
  - doi: 10.1093/nar/gkp335
    metadata:
      abstract: The MEME Suite web server provides a unified portal for online discovery
        and analysis of sequence motifs representing features such as DNA binding
        sites and protein interaction domains. The popular MEME motif discovery algorithm
        is now complemented by the GLAM2 algorithm which allows discovery of motifs
        containing gaps. Three sequence scanning algorithms - MAST, FIMO and GLAM2SCAN
        - allow scanning numerous DNA and protein sequence databases for motifs discovered
        by MEME and GLAM2. Transcription factor motifs (including those discovered
        using MEME) can be compared with motifs in many popular motif databases using
        the motif database scanning algorithm Tomtom. Transcription factor motifs
        can be further analyzed for putative function by association with Gene Ontology
        (GO) terms using the motif-GO term association tool GOMO. MEME output now
        contains sequence LOGOS for each discovered motif, as well as buttons to allow
        motifs to be conveniently submitted to the sequence and motif database scanning
        algorithms (MAST, FIMO and Tomtom), or to GOMO, for further analysis. GLAM2
        output similarly contains buttons for further analysis using GLAM2SCAN and
        for rerunning GLAM2 with different parameters. All of the motif-based tools
        are now implemented as web services via Opal. Source code, binaries and a
        web server are freely available for noncommercial use at http://meme.nbcr.net.
      authors:
      - name: Bailey T.L.
      - name: Boden M.
      - name: Buske F.A.
      - name: Frith M.
      - name: Grant C.E.
      - name: Clementi L.
      - name: Ren J.
      - name: Li W.W.
      - name: Noble W.S.
      citationCount: 4500
      date: '2009-08-04T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MEME Suite: Tools for motif discovery and searching'
    note: null
    pmcid: null
    pmid: '19458158'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  - Suite
  topic:
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: DNA binding sites
    uri: http://edamontology.org/topic_3125
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-04-29T09:58:49Z'
  biotoolsCURIE: biotools:sparse
  biotoolsID: sparse
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: miladim@informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Milad Miladi
    note: null
    orcidid: http://orcid.org/0000-0002-0173-3009
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University Freiburg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: rnateam
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Very efficient structure-based alignment of RNAs.
  documentation:
  - note: null
    type:
    - General
    url: http://www.bioinf.uni-freiburg.de/Software/SPARSE/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: A simultaneous alignment and folding tool with quadratic complexity
    operation:
    - term: Structure-based sequence alignment
      uri: http://edamontology.org/operation_0294
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: RNA structure
        uri: http://edamontology.org/data_1465
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
  homepage: http://www.bioinf.uni-freiburg.de/Software/SPARSE
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2019-01-11T00:33:45Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: SPARSE
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: rnateam
  publication:
  - doi: 10.1093/bioinformatics/btv185
    metadata:
      abstract: '© The Author 2015. Published by Oxford University Press.Motivation:
        RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard
        for their analysis based on simultaneous alignment and folding suffers from
        extreme time complexity of O(n6). Subsequently, numerous faster ''Sankoff-style''
        approaches have been suggested. Commonly, the performance of such methods
        relies on sequence-based heuristics that restrict the search space to optimal
        or near-optimal sequence alignments; however, the accuracy of sequencebased
        methods breaks down for RNAs with sequence identities below 60%. Alignment
        approaches like LocARNAthat do not require sequence-based heuristics, have
        been limited to high complexity (> quartictime). Results: Breaking this barrier,
        we introduce the novel Sankoff-style algorithm ''sparsified prediction and
        alignment of RNAs based on their structure ensembles (SPARSE)'', which runs
        in quadratic time without sequence-based heuristics. To achieve this low complexity,
        on par with sequence alignment algorithms, SPARSE features strong sparsification
        based on structural properties of the RNA ensembles. Following PMcomp, SPARSE
        gains further speed-up from lightweight energy computation. Although all existing
        lightweight Sankoff-style methods restrict Sankoff''s original model by disallowing
        loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the
        lightweight energy model completely for the first time. Compared with LocARNA,
        SPARSE achieves similar alignment and better folding quality in significantly
        less time (speedup: 3.7). At similar run-time, it aligns low sequence identity
        instances substantially more accurate than RAF, which uses sequence-based
        heuristics.'
      authors:
      - name: Will S.
      - name: Otto C.
      - name: Miladi M.
      - name: Mohl M.
      - name: Backofen R.
      citationCount: 24
      date: '2015-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'SPARSE: Quadratic time simultaneous alignment and folding of RNAs without
        sequence-based heuristics'
    note: null
    pmcid: PMC4514930
    pmid: '25838465'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - 1.8.9
- accessibility: null
  additionDate: '2016-04-29T09:57:28Z'
  biotoolsCURIE: biotools:exparna-p
  biotoolsID: exparna-p
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University Freiburg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: rnateam
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: schmiedc@informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Christina Otto
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: schmiedc@informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Christina Otto
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Simultaneous exact pattern matching and folding of RNAs.
  documentation:
  - note: null
    type:
    - General
    url: http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: ExpaRNA 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.
    operation:
    - term: Structure-based sequence alignment
      uri: http://edamontology.org/operation_0294
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
  homepage: http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P/
  homepage_status: 0
  language: []
  lastUpdate: '2019-01-11T00:06:26Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: ExpaRNA-P
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: rnateam
  publication:
  - doi: 10.1186/s12859-014-0404-0
    metadata:
      abstract: '© Otto et al.; licensee BioMed Central.Background: Identifying sequence-structure
        motifs common to two RNAs can speed up the comparison of structural RNAs substantially.
        The core algorithm of the existent approach solves this problem for input
        structures. However, such structures are rarely known; moreover, predicting
        them computationally is no rescue, since single sequence structure prediction
        is highly unreliable. Results: The novel algorithm computes exactly matching
        sequence-structure motifs in entire Boltzmann-distributed structure ensembles
        of two RNAs; thereby we match and fold RNAs simultaneously, analogous to the
        well-known "simultaneous alignment and folding" of RNAs. While this implies
        much higher flexibility compared to, has the same very low complexity (quadratic
        in time and space), which is enabled by its novel structure ensemble-based
        sparsification. Furthermore, we devise a generalized chaining algorithm to
        compute compatible subsets of ''s sequence-structure motifs. Resulting in
        the very fast RNA alignment approach, we utilize the best chain as anchor
        constraints for the sequence-structure alignment tool. is benchmarked in several
        variants and versus state-of-the-art approaches. In particular, we formally
        introduce and evaluate strict and relaxed variants of the problem; the latter
        makes the approach sensitive to compensatory mutations. Across a benchmark
        set of typical non-coding RNAs, has similar accuracy to but is four times
        faster (in both variants), while it achieves a speed-up over 30-fold for the
        longest benchmark sequences (≈400nt). Finally, different variants enable tailoring
        of the method to specific application scenarios. and are distributed as part
        of the package. The source code is freely available at. Conclusions: ''s novel
        ensemble-based sparsification reduces its complexity to quadratic time and
        space. Thereby, significantly speeds up sequence-structure alignment while
        maintaining the alignment quality. Different variants support a wide range
        of applications.'
      authors:
      - name: Otto C.
      - name: Mohl M.
      - name: Heyne S.
      - name: Amit M.
      - name: Landau G.M.
      - name: Backofen R.
      - name: Will S.
      citationCount: 12
      date: '2014-12-31T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'ExpaRNA-P: Simultaneous exact pattern matching and folding of RNAs'
    note: null
    pmcid: PMC4302096
    pmid: '25551362'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - 1.8.9
- accessibility: null
  additionDate: '2016-04-29T10:12:35Z'
  biotoolsCURIE: biotools:carna
  biotoolsID: carna
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University Freiburg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: rnateam
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Alignment of RNA structure ensembles.
  documentation:
  - note: null
    type:
    - General
    url: http://rna.informatik.uni-freiburg.de/Help.jsp
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: CARNA 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.
    operation:
    - term: Structure-based sequence alignment
      uri: http://edamontology.org/operation_0294
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: Image format
        uri: http://edamontology.org/format_3547
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: http://rna.informatik.uni-freiburg.de/CARNA/
  homepage_status: 0
  language: []
  lastUpdate: '2019-01-09T15:29:49Z'
  license: null
  link: []
  maturity: Mature
  name: CARNA web server
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: rnateam
  publication:
  - doi: 10.1093/nar/gks491
    metadata:
      abstract: Due to recent algorithmic progress, tools for the gold standard of
        comparative RNA analysis, namely Sankoff-style simultaneous alignment and
        folding, are now readily applicable. Such approaches, however, compare RNAs
        with respect to a simultaneously predicted, single, nested consensus structure.
        To make multiple alignment of RNAs available in cases, where this limitation
        of the standard approach is critical, we introduce a web server that provides
        a complete and convenient interface to the RNA structure alignment tool 'CARNA'.
        This tool uniquely supports RNAs with multiple conserved structures per RNA
        and aligns pseudoknots intrinsically; these features are highly desirable
        for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots.
        We represent structural input and output information as base pair probability
        dot plots; this provides large flexibility in the input, ranging from fixed
        structures to structure ensembles, and enables immediate visual analysis of
        the results. In contrast to conventional Sankoff-style approaches, 'CARNA'
        optimizes all structural similarities in the input simultaneously, for example
        across an entire RNA structure ensemble. Even compared with already costly
        Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem
        by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA'
        is specialized to the alignment of RNAs with several conserved structures,
        its performance on RNAs in general is on par with state-of-the-art general-purpose
        RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server
        is freely available at http://rna.informatik.uni-freiburg.de/CARNA. © 2012
        The Author(s).
      authors:
      - name: Sorescu D.A.
      - name: Mohl M.
      - name: Mann M.
      - name: Backofen R.
      - name: Will S.
      citationCount: 18
      date: '2012-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: CARNA-alignment of RNA structure ensembles
    note: null
    pmcid: PMC3394245
    pmid: '22689637'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - 1.2.5
- accessibility: null
  additionDate: '2016-04-29T10:00:44Z'
  biotoolsCURIE: biotools:locarna-p
  biotoolsID: locarna-p
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University Freiburg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: rnateam
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Probabilistic structure-based multiple alignment of RNAs.
  documentation:
  - note: null
    type:
    - General
    url: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: LocARNA simultaneously folds and aligns input sequences. Specifications
      of additional constraints or fixed input structures are possible.
    operation:
    - term: Structure-based sequence alignment
      uri: http://edamontology.org/operation_0294
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: RNA structure
        uri: http://edamontology.org/data_1465
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
  homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2018-12-30T16:57:20Z'
  license: null
  link: []
  maturity: Mature
  name: LocARNA-P
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: rnateam
  publication:
  - doi: 10.1261/rna.029041.111
    metadata:
      abstract: Current genomic screens for noncoding RNAs (ncRNAs) predict a large
        number of genomic regions containing potential structural ncRNAs. The analysis
        of these data requires highly accurate prediction of ncRNA boundaries and
        discrimination of promising candidate ncRNAs from weak predictions. Existing
        methods struggle with these goals because they rely on sequencebased multiple
        sequence alignments, which regularly misalign RNA structure and therefore
        do not support identification of structural similarities. To overcome this
        limitation, we compute columnwise and global reliabilities of alignments based
        on sequence and structure similarity; we refer to these structure-based alignment
        reliabilities as STARs. The columnwise STARs of alignments, or STAR profiles,
        provide a versatile tool for the manual and automatic analysis of ncRNAs.
        In particular, we improve the boundary prediction of the widely used ncRNA
        gene finder RNAz by a factor of 3 from a median deviation of 47 to 13 nt.
        Post-processing RNAz predictions, LocARNA-P's STAR score allows much stronger
        discrimination between true- and false-positive predictions than RNAz's own
        evaluation. The improved accuracy, in this scenario increased from AUC 0.71
        to AUC 0.87, significantly reduces the cost of successive analysis steps.
        The ready-to-use software tool LocARNA-P produces structure-based multiple
        RNA alignments with associated columnwise STARs and predicts ncRNA boundaries.
        We provide additional results, a web server for LocARNA/LocARNA-P, and the
        software package, including documentation and a pipeline for refining screens
        for structural ncRNA, at http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.
      authors:
      - name: Will S.
      - name: Joshi T.
      - name: Hofacker I.L.
      - name: Stadler P.F.
      - name: Backofen R.
      citationCount: 203
      date: '2012-05-01T00:00:00Z'
      journal: RNA
      title: 'LocARNA-P: Accurate boundary prediction and improved detection of structural
        RNAs'
    note: null
    pmcid: PMC3334699
    pmid: '22450757'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - 1.8.9
- accessibility: null
  additionDate: '2016-04-29T09:39:30Z'
  biotoolsCURIE: biotools:locarna
  biotoolsID: locarna
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University Freiburg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: RNA tools and software consortium
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Documentor
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: rna@rna.informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Rolf Backofen
    note: null
    orcidid: http://orcid.org/0000-0001-8231-3323
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: will@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: Sebastian Will
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Structure-based multiple alignment of RNAs.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/s-will/LocARNA/blob/master/README
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: LocARNA simultaneously folds and aligns input sequences. Specifications
      of additional constraints or fixed input structures are possible.
    operation:
    - term: Structure-based sequence alignment
      uri: http://edamontology.org/operation_0294
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: RNA structure
        uri: http://edamontology.org/data_1465
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
  homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2018-12-24T21:45:33Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: LocARNA
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: rnateam
  publication:
  - doi: 10.1371/journal.pcbi.0030065
    metadata:
      abstract: 'The RFAM database defines families of ncRNAs by means of sequence
        similarities that are sufficient to establish homology. In some cases, such
        as microRNAs and box H/ACA snoRNAs, functional commonalities define classes
        of RNAs that are characterized by structural similarities, and typically consist
        of multiple RNA families. Recent advances in high-throughput transcriptomics
        and comparative genomics have produced very large sets of putative noncoding
        RNAs and regulatory RNA signals. For many of them, evidence for stabilizing
        selection acting on their secondary structures has been derived, and at least
        approximate models of their structures have been computed. The overwhelming
        majority of these hypothetical RNAs cannot be assigned to established families
        or classes. We present here a structure-based clustering approach that is
        capable of extracting putative RNA classes from genome-wide surveys for structured
        RNAs. The LocARNA (local alignment of RNA) tool implements a novel variant
        of the Sankoff algorithm that is sufficiently fast to deal with several thousand
        candidate sequences. The method is also robust against false positive predictions,
        i.e., a contamination of the input data with unstructured or nonconserved
        sequences. We have successfully tested the LocARNA-based clustering approach
        on the sequences of the RFAM-seed alignments. Furthermore, we have applied
        it to a previously published set of 3,332 predicted structured elements in
        the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005) Noncoding
        RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2): i77-i78). In
        addition to recovering, e.g., tRNAs as a structure-based class, the method
        identifies several RNA families, including microRNA and snoRNA candidates,
        and suggests several novel classes of ncRNAs for which to date no representative
        has been experimentally characterized. © 2007 Will et al.'
      authors:
      - name: Will S.
      - name: Reiche K.
      - name: Hofacker I.L.
      - name: Stadler P.F.
      - name: Backofen R.
      citationCount: 341
      date: '2007-04-01T00:00:00Z'
      journal: PLoS Computational Biology
      title: Inferring noncoding RNA families and classes by means of genome-scale
        structure-based clustering
    note: null
    pmcid: PMC1851984
    pmid: '17432929'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - 1.8.9
next: null
previous: null
