[Bioclusters] sequence analysis

[Andrew Shewmaker]

Hello,

I'm a linux cluster admin and I'm trying to help a biologist find the right
software for his needs.  He is currently using clustalw to process multiple
alignments (~ 400 sequences), and he needs a good phylogenic tool.  He isn't
very computer savvy and I don't have a background in biology, so I'm finding
it difficult to help him.  I've been reading the clustalw docs and looking at
phylip, but I thought I would ask for help.

Basically, he wants to put sequences with a given % similarity or greater into
a groups.  He also wants to identify the least divergent group member (i.e.,
which sequence has the highest average similarity to the others in the
group).

I've looked at Jalview (http://www2.ebi.ac.uk/~michele/jalview/) and a few
other programs that will draw a tree and show distances, but I'm a little
fuzzy on how distance relates to similarity.  I think I read in the clustalw
docs that distance was 1.0 - similarity/100.

Thanks for any help,

Andrew

--
Andrew Shewmaker
Associate Engineer, INEEL
Phone: 1-208-526-1415