Phylogenetic Trees of Proteins?

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In article <5u8hqg$a4b at nntp3.u.washington.edu> joe at evolution.genetics.washington.edu (Joe Felsenstein) wrote:
> In article <btsmith-2508971738550001 at rhizobium.mit.edu>,
> Bradley T. Smith <btsmith at mit.edu> wrote:
> >

In article <btsmith-2508971738550001 at rhizobium.mit.edu>,
Bradley T. Smith <btsmith at mit.edu> wrote:
>
>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.

Thanks for the opportunity for a little publicity.  Try looking at the
Phylogeny Programs page on our PHYLIP web site.  It is:

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

At present it lists over 100 phylogeny programs, many of them free.
You could of course start with the first one listed (which just happens to
be ours ...

---- 
Joe Felsenstein         joe at genetics.washington.edu     (IP No. 128.95.12.41)
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA