Clustal

Clustal is a widely used multiple alignment programme with free packages that can rapidly and simply align hundreds of nucleic acid or amino acid sequences.

There are two main variations (bold) and other "improved" variations:

• ClustalW: command line interface.
• ClustalX: This is version has a graphical user interface. It is availabe for Windows, Mac OS and Unix/Linux
• ClustalV
• ClustalG: The package is a rewrite of the well-known Clustal series of alignment packages. The main new feature of ClustalG is the recognition of input word sequences of up to six characters.

Input/Output

This program accept 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:

1. Do a pairwise alignment
2. Create phylogenetic tree (or use user define 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 guild 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.

Settings

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

• Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, and Thompson JD (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research 31:3497-3500.
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24:4876-4882.
• Higgins DG, Thompson JD, and Gibson TJ (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:383-402.
• Thompson JD, Higgins DG, and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673-4680.
• Higgins DG, Bleasby AJ, and Fuchs R (1992). CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8:189-191.
• Higgins DG and Sharp PM (1989). Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5:151-153.
• Higgins DG and Sharp PM (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244.

Download

• This programme (latest version is 1.83) is available from European Bioinformatics Institute ftp server. Choose unix for Unix/Linux, mac for Mac OS, or dos for Windows.

External links

• Wikipedia article on Clustal
• ClustalW — from the EMBL
• ClustalX — from Strasbourg Bioinformatics Platform - France
• ClustalV — from INFOBIOGEN