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ClustalW2

ClustalW2

Tools for multiple protein sequence alignment. The algorithm uses a guide tree in alignment creation. There are two separate flavors of Clustal 2: Clustal W, the command-line version and Clustal X, the graphical version.

Topic

Proteomics

Details

  • Operation: Multiple sequence alignment
  • Input: Protein sequence in FASTA format
  • Output: ClustalW with character counts; ClustalW; Pearson/FASTA; MSF; NEXUS; PHYLIP; SELEX; STOCKHOLM; VIENNA
  • Software interface: command-line interface; graphical user interface
  • Language: C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU Lesser GPL
  • Cost: Free
  • Version name: 2.1
  • Maturity: Mature
  • Credit: Science Foundation Ireland
  • Contact: http://www.clustal.org/clustal2/#Contact
  • Collection: Clustal

Publications

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG "Clustal W and Clustal X version 2.0." https://doi.org/10.1093/bioinformatics/btm404
PMID: 17846036


Higgins DG, Sharp PM "CLUSTAL: a package for performing multiple sequence alignment on a microcomputer" Gene, 73, 237-244 https://doi.org/10.1016/0378-1119(88)90330-7
PMID: 3243435


Higgins DG, Thompson JD, Gibson TJ "Using CLUSTAL for multiple sequence alignments" Methods Enzymol., 266, 383-402 https://doi.org/10.1016/S0076-6879(96)66024-8
PMID: 8743695


Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ "Multiple sequence alignment with Clustal X" Trends Biochem Sci., 23, 403-405 https://doi.org/10.1016/s0968-0004(98)01285-7
PMID: 9810230


Higgins,DG and Sharp,PM "Fast and sensitive multiple sequence alignments on a microcomputer" Comput. Appl. Biosci., 5, 151-153 https://doi.org/10.1093/bioinformatics/5.2.151
PMID: 2720464


Higgins DG, Bleasby AJ, Fuchs R "CLUSTAL V: improved software for multiple sequence alignment" Comput. Appl. Biosci., 8, 189-191 https://doi.org/10.1093/bioinformatics/8.2.189
PMID: 1591615


Thompson JD, Higgins DG, Gibson TJ "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 1994 Nov 11;22(22):4673-80. https://doi.org/10.1093/nar/22.22.4673
PMID: 7984417
PMCID: PMC308517


Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools" Nucleic Acids Res., 25, 4876-4882 https://doi.org/10.1093/nar/25.24.4876
PMID: 9396791
PMCID: PMC147148


Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD "Multiple sequence alignment with the Clustal series of programs" Nucleic Acids Res., 31, 3497-3500 https://doi.org/10.1093/nar/gkg500
PMID: 12824352
PMCID: PMC168907


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