ClustalX

ClustalX is the graphical user interface version of Clustal. It is availabe for free for Windows, Mac OS and Unix/Linux.

Using ClustalX to build Phylogenetic trees

Note: This is only to give the user a very basic introduction to phylogenetic tree building techniques.

Calculating a phylogenetic tree using ClustalX involves the five steps listed below (all of the necessary commands are located in the 'Trees' menu):

Remove the regions of the alignment with gaps: select 'delete positions with gaps'.
If your sequences are less than ~95% identical, you should choose to correct your distance measures for mutiple substitutions: 'correct for multiple substitutions'.
Make sure you have the correct format for the output:
- follow the 'output format link';
- change 'bootstrap label options' from 'branches' to 'nodes'; and
- close
Calculate the tree by selecting 'bootstrap NJ tree'.
View the results in a tree-viewing programme, such as Treeview or NJplot.

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.
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.

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.