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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Andrew Rambaut, EMAIL - Andrew.Rambaut at zoology.ox.ac.uk
Zoology Department, WWW - http://evolve.zoo.ox.ac.uk/
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