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Clustal

From Biocrawler, the free encyclopedia.

Clustal This is a widely used multiple alignment program. The latest version is 1.83. There are two main variations:

ClustalW: command line interface.

ClustalX: This is version have graphical user interface. It is availabe for Windows, Mac OS and Unix/Linux

This program is available from European Bioinformatics Institute ftp server (ftp://ftp.ebi.ac.uk/pub/software/). Choose unix for Unix/Linux, mac for Mac OS, or dos for Windows

Contents

1 Input/Output

2 Multiple sequence alignment

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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.

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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 Alignmetn from guide tree" and "Produce guild tree only"

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Profile alignments

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Setting

User can align the sequences with default setting. But sometimes it's useful to customers your own parameters.

The main parameters are the gap opening penalty, gap extension penalty

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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, 24:4876-4882.

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