Computing degrees of sequence conservation in multialignedsequences

felipe wettstein felipe at spin.ch
Tue Jul 25 10:16:04 EST 2000


>         I'm looking for a non-commercial software for UNIX or Mac (also a
> web server) that:
>         1) uses a multiple sequence alignment in GCG form as input.
>         2) output the degree of sequence conservation in the multialignment
> in order to find (and define) in an objective way the limits of similar
> sequence regions.
>         In fact, I'm looking for a UNIX or Mac soft similar to the
> described by Friemann & Schmitz in "A new approach for displaying
> identities and differences among aligned amino acid sequences. (1992).
> CABIOS 8(3):261-165."

you could probably use arb, it does alignements and phylogenetic trees,
with proteins and dna, there are so many feautures that i imagine that
it can also do things as you want them, you must trie to find out.
arb is free for linux, i guess it would also work on unix (i apriciate
your two OS options, me i have to work the whole f. day with wintel crap
(and 1 linux/amd machine of course)).

saludos desde alemania



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