Clustal

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CLUSTAL
Developer(s) <templatestyles src="Plainlist/styles.css"/>
  • Des Higgins
  • Fabian Sievers
  • David Dineen
  • Andreas Wilm (all at the Conway Institute, UCD)
Stable release 1.2.0 / 12 June 2013; 10 years ago (2013-06-12)
Written in C++
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
Licence GNU General Public License, version 2[1]
Website www.clustal.org/omega/
ClustalW/ClustalX
Developer(s) Gibson T. (EMBL), Thompson J. (CNRS), Higgins D. (UCD)
Stable release 2.1 / 17 November 2010; 13 years ago (2010-11-17)
Written in C++
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
Licence GNU Lesser General Public License [2]
Website www.clustal.org

In Bioinformatics Clustal is a series of widely used computer programs for multiple sequence alignment.[3] There have been many incarnations of Clustal that are listed below:

  • Clustal: The original software for progressive alignment based on a phylogenetic tree.[4]
  • ClustalV: A rewrite of the original Clustal package that included phylogenetic tree reconstruction on the final alignment for the first time.[5]
  • ClustalW: command line interface[6]
  • ClustalX: This version has a graphical user interface.[7]
  • Clustal Omega: Command line-only program.[8][9]

The papers describing the clustal software have been very highly cited, with two appearing in a list of the most cited papers of all time.[10]

The more recent version of the software available for Windows, Mac OS, and Unix/Linux. This program is available from the Clustal Homepage or European Bioinformatics Institute ftp server.

Input/Output

This program accepts a wide range of input formats, including NBRF/PIR, FASTA, EMBL/Swiss-Prot, Clustal, GCC/MSF, GCG9 RSF, and GDE.

The output format can be one or many of the following: Clustal, NBRF/PIR, GCG/MSF, PHYLIP, GDE, or NEXUS.

Multiple sequence alignment

There are three main steps:

  1. Do a pairwise alignment
  2. Create a guide tree (or use a user-defined tree)
  3. Use the guide tree to carry out a multiple alignment

These are done automatically when you select "Do Complete Alignment". Other options are "Do Alignment from guide tree and phylogeny" and "Produce guide tree only".

Setting

Users can align the sequences using the default setting, but occasionally it may be useful to customize one's own parameters.

The main parameters are the gap opening penalty, and the gap extension penalty.

Names

The guide tree in the initial programs was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL.[11]cf.[12] The first four versions in 1988 had Arabic numerals (1 to 4), whereas with the fifth version Des Higgins switched to Roman numeral V in 1992.[11]cf.[13][14] In 1994 and in 1997, for the next two versions, the letters after the letter V were used and made to correspond to W for Weighted and X for X Window.[11]cf.[15][16] The name omega was chosen to mark a change from the previous ones.[11]

See also

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References

  1. ↑ See file COPYING, in source archive [1]. Accessed 2014-01-15.
  2. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  3. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  5. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  6. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  7. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  10. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  11. ↑ 11.0 11.1 11.2 11.3 Des Higgins, presentation at the SMBE 2012 conference in Dublin.
  12. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  13. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  14. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  15. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  16. ↑ Lua error in package.lua at line 80: module 'strict' not found.

External links

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