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 multiple 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
- 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.