help with DNA sequence analysis software

[Ben Waggoner]

On Sat, 3 Feb 1996, Jerry Bricker wrote:

> > Soon I hope to have a number of legume DNA sequences that I would like to
> > compare.  I am aware of a mainframe software package (from Wisconsin, I
> > believe) that is designed to aline and compare sequences and produce
> > concensus sequences, etc.
> >
> > I would like to obtain information on the availability of PC or MAC based
> > software programs that will aline and compare nucleic acid sequences and
> > produce concensus sequences.
> >
> > If you have information about any software that can do this I would be
> > grateful if you would share this with me.
> >
>
> It is nice living in the balmy south.  Our thermometers recorded a
> positive heat wave of -20 degrees F this morning.  Glad we don't have it
> as bad as N. Dakota.  Now if you want to talk about wind, that's an
> entirely different matter!

I'm still new at the molecular phylogeny trade, so I don't have any great
recommendations based on personal experience. But. . .
On the WWW, check out
    http://evolution.genetics.washington.edu/software.html
    http://taxonomy.zoology.gla.ac.uk/software.html
    http://phylogeny.arizona.edu/tree/programs/programs.html
for listings and reviews of software, including ftp sites from which to
download it. There's a lot of programs available for free; I'm still finding
out the merits and demerits of each.

It's about 40 degrees F and drizzling here in Berkeley. Nyaaah.

Ben Waggoner
Dept. of Integrative Biology
University of California
Berkeley, CA 94720 USA
bmw at uclink2.berkeley.edu

The Professor got up once in the B.A., and declared that apes had
hippopotamus majors in their brains, just like men have. Which was a
terrible thing to say; for if it were so, what would become of the faith,
hope and charity of immortal millions. (C. Kingsley, 'The Water Babies')