Clustal Information & Clustal Links at HealthHaven.com

Clustal
Developer(s)	Gibson T. (EMBL), Thompson J. (CNRS), Higgins D. (UCD)
Stable release	2.0.12 / 2009-09-24; 2 months ago
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 2.0.^[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.

[edit] 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, NEXUS.

There are three main steps:

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

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.

^ 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. PMID 12824352.
^ 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). "ClustalW2 and ClustalX version 2". Bioinformatics 23 (21): 2947-2948. doi:10.1093/bioinformatics/btm404. PMID 17846036.
^ 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. PMID 9396791.