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Clustal is a widely used multiple sequence alignment computer program. The latest version is 1.83. There are two main variations:
- ClustalW: command line interface
- ClustalX: This version has a graphical user interface. It is availabe for Windows, Mac OS and Unix/Linux.
This program is available from European Bioinformatics Institute ftp server. Choose unix for Unix/Linux, mac for Mac OS, or dos for Windows.
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.
Multiple sequence alignment
There are 3 main steps:
- Do a pairwise alignment
- Create phylogenetic tree (or use user define tree)
- 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".
Profile alignments
Pairwise alignments are computed for all against all sequences, and similarities are stored in a matrix. This is then converted into a distance matrix, where the distance measures reflect the evolutionary distance between each pair of sequences.
From this distance matrix, a guide tree, or phylogenetic tree, for the order in which pairs of sequences are to be aligned and combined with previous alignments is constructed using a neighbour-joining clustering algorithm. Sequences are progessively aligned at each branch point, starting from the least distant pair of sequences.
Setting
Users can align the sequences using the default setting. But sometimes it's useful to customize your own parameters.
The main parameters are the gap opening penalty, and the gap extension penalty.
References
Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25:4876-4882.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
External links
"Clustal"