Clustal

Clustal

Developer(s)	Gibson T. (EMBL), Thompson J. (CNRS), Higgins D. (UCD)
Stable release	2.1 / 17 November 2010; 11 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:

• ClustalW: command line interface
• ClustalX: This version has a graphical user interface.^[3] It is 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 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

• Sequence alignment software
• T-Coffee
• Align-m
• DIALIGN-T
• DIALIGN-TX
• JAligner
• MAFFT
• MAVID
• MUSCLE
• ProbCons

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

• Clustal Homepage (free Unix/Linux, Mac, and Windows download)
• ClustalW and ClustalX mirror at the EBI (free Unix/Linux, Mac, and Windows download)
• "Accelerating Intensive Applications at 10x-50x Speedup to Remove Bottlenecks in Computational Workflows" — White Paper by Progeniq Pte Ltd.
• Multiple Sequence Alignment by CLUSTALW