Section 12-3: Phylogeny

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The program pileup (see above ) is used to create a multiple sequence alignment. Then, the program distances is used to compute the distances in between the different aligned files, and growtree can draw a figure which shows the sequences arranged in a tree which represents the distances as computed from the alignment.

NOTE: This way of tree creation depends entirely on the alignment. If the similarity of the sequences considered is low, the alignment produced by 'pileup' might be faulty and require manual refinement. The resulting tree must be considered to be of significantly reduced value as possible errors will effect the resulting tree significantly.

PAUP-based Methods

At the time of writing, the programs paupsearch and paupdisplay were unfortunately not included in the GCG distribution. Phylip (by J.Felsenstein) and other packages are also available on personal computers and macintoshes. Various public domain and shareware programs might be useful to you. Refer to the discussion on additonal software earlier in the BioCompanion for benefits and problems of adding software.