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

Francois Jeanmougin pingouin at chouchen.u-strasbg.fr
Fri Aug 1 02:24:08 EST 1997


[Posted and mailed]

In article <33e48227.9371298 at news.su.se>,
	ev-michael at SPAMSTOPnrm.se (Mike Noren) writes:
[...]
> ClustalW 1.6 usually does an acceptable job, even with sequences rich
> in gaps. With sequences of very different lengths it tends to fail
> miserably, though, and I'm not sure how it'll handle very small
> sequences like yours. Profile alignment usually works in v1.6, which
> was not the case in v1.5.
[...]
	ClustalW is now version 1.7 and accepts GCG9 multiple sequence
file formats (MSF/RSF) as input. Also, we have done some improvements on
the alfgorithm, especially for highly divregent sequences. ClustalW1.6
has a bug in the GOP calculation and misplaced some residues at 
gap opening positions.

	Please update your programme from :

	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/

	Also, give a try to ClustalX (1.5b), which is a GUI for ClustalW 
and has some analysis tools.

	Feel free to contact me for any question.
							François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
"Ce sont des désespoirs d'intellectuels ennuyés, ou des ennuis 
d'intellectuels désespérés, comme vous voulez, comme vous voulez" M. Benin



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