Clustal

Clustal
Developer(s) Gibson T. (EMBL), Thompson J. (CNRS), Higgins D. (UCD)
Stable release 2.1 / 17 November 2010; 14 months ago (2010-11-17)
Written in C++
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
Licence Free for academic users
Website Clustal

Clustal is a widely used multiple sequence alignment computer program.[1] The latest version is 2.1.[2] There are two main variations:

This program is available from the Clustal Homepage or European Bioinformatics Institute ftp server.

Contents

Input/Output

This program accepts a wide range on input format. Included NBRF/PIR, FASTA, EMBL/Swissprot, 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 phylogenetic tree (or use a user-defined tree)
  3. Use the phylogenetic 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 "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.

See also

References

  1. ^ Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003). "Multiple sequence alignment with the Clustal series of programs". Nucleic Acids Res 31 (13): 3497–3500. doi:10.1093/nar/gkg500. PMC 168907. PMID 12824352. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=168907. 
  2. ^ 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 (2007). "ClustalW and ClustalX version 2". Bioinformatics 23 (21): 2947–2948. doi:10.1093/bioinformatics/btm404. PMID 17846036. 
  3. ^ Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools". Nucleic Acids Research 25 (24): 4876–4882. doi:10.1093/nar/25.24.4876. PMC 147148. PMID 9396791. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=147148. 

External links