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.
btsmith at mit.edu