Phylogenetic Trees of Proteins?

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In article <andrew.rambaut-ya023380003008971410260001 at news.ox.ac.uk> andrew.rambaut at zoology.oxford.ac.uk (Andrew Rambaut) wrote:
> 
> > I am looking for a program (preferable share- or freeware) that will
> > construct phylogenetic trees (rooted and/or unrooted) using a collection


> I am looking for a program (preferable share- or freeware) that will
> construct phylogenetic trees (rooted and/or unrooted) using a collection
> of protein sequences.
> 
> Our lab uses Lasergene from DNASTAR which has a utility within MegAlign
> which can construct trees.  However, I am not satisfied with the trees
> that I get using this utility.  The program uses divergence values, which
> it determines, to construct the tree.  Many proteins, while moderately
> similar to the rest of the collection, are deemed 100% divergent and are
> put on their own branch.
> 
> I find this to be somewhat annoying, and I hope that there are alternative
> methods that I can use to construct a tree.

Try using Jun Adachi's MolPhy package. There is a maximum likelihood tree
reconstruction program in it called protml (see site below).

A good list of phylogenetics software can be found at Joe Felsenstein's site:

http://evolution.genetics.washington.edu/phylip/software.html

A.

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