In article <5n6aj9$9on at n.ruf.uni-freiburg.de>,
vonrhein at bio6.chemie.uni-freiburg.de (Clemens Vonrhein) writes:
> Is there a (free?) alignment software which can use an existing
> multiple alignment - and keep it fixed - to align several other
> sequences to?
>> I *think* MSA can handle this? But it's sloooow ...
Well, I'm not using a bulk mail programme but... ClustalW and
ClustalX can do that. Using the profile alignment system, you input
an alignment which is used as a profile, and you can easily (very
easily with ClustalX) add new sequences to a fixed alignment. Note
that if the new sequence diverge, you will have to add gaps to your
existing profile, but the alignement between original sequences is
maintained.
Just try ClustalX and let us know:
ftp://ftp-igbmc.u-strasbg.fr/ClustalX/
Hope this helps,
Francois.
P.S.: The profile alignement method from Clustal is not so slow,
it depends of the machine and system you have.
--
Francois Jeanmougin | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine)
