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Phylogenetic Trees of Proteins?

Bradley T. Smith btsmith at mit.edu
Mon Aug 25 18:31:08 EST 1997


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.

Thnak you, in advence, for you assistance.

-Brad Smith
 btsmith at mit.edu

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