Phylogenetic Analysis

Exercise

Construct a phylogenetic tree based on a multiple alignment of HIV protein sequences. You will use the "neighbor joining" algorithm implemented in the ClustalX program for tree-reconstruction and the "unrooted" program for viewing the result.

Transparencies

All transparencies for the lecture on phylogenetic reconstruction are in your course material. BUT there are errors on two slides dealing with maximum parsimony. The correct versions are here:

Maximum parsimony 1 (phylogenetic reconstruction, Fitch)
Maximum parsimony 2 (reconstruction of ancestors)

Downloadable software

Tree Viewers

• TreeView: tree-viewer with user-friendly, graphical interface.
• PhyloDraw: another tree-viewer.

Tools for inferring and interpreting phylogenetic trees

• ClustalX: multiple alignment and distance-based tree-reconstruction (neighbor joining).
• Phylip: reconstruct trees using maximum likelihood, parsimony, or distance methods.
• PAUP*: reconstruct and analyze trees using maximum likelihood, parsimony, or distance methods.
• PAML: analyze phylogenetic hypotheses using maximum likelihood.

Additional resources

• An extensive list of downloadable software for phylogenetic analysis.
• Online tutorial in tree-reconstruction. With illustrative java-applets.
• Another tree tutorial at the HIV sequence database at Los Alamos National Laboratory.