Which is the MULTIPLE ALIGNMENT code that can be INTERFACED most EASILY ?

Georg Fuellen fuellen at REPLY-TO_HEADER_HAS_BEEN_SET_IN_ORIGINAL_POST_OR_JUST_REMOVE_THIS_SPAM_BLOCKERtechfak.uni-bielefeld.de
Wed Jul 30 16:15:55 EST 1997


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,
Georg Fuellen
Univ. Bielefeld, Research Group in Practical Comp. Science,
http://www.techfak.uni-bielefeld.de/bcd/welcome.html
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.






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