I'm eager to hear your experiences and advice regarding multiple alignment
software, and interfacing to it. Just reply straight away, do it now :)
I'm looking for easily interface'able code for
a) the heuristic guide-tree driven alignment of 10-50 very short
(10-20 residues) biosequences,
b) the alignment of 2 profiles (using a profile alignment like ClustalW
does; again, the length is small),
c) the optimal or near-optimal alignment of such sequences using sum-of-pairs.
E.g., would you recommand ClustalW / MSA ? Or MAP ? Or MultAlin ?
Any other tools you tried ?
Do you have unreleased code for the task ?
all the best wishes,
Univ. Bielefeld, Research Group in Practical Comp. Science,
P.S. This article shall not be archived (I've set ``x-no-archive: yes'')
to avoid unsolicited commercial email to my address. In any case, commercial
junk mail will trigger an appropriate action.