ClustalW problem

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Fri Dec 4 03:45:16 EST 1998


In article <bpmurray*STUFFER*-0312981314230001 at macmac-2.ucsf.edu>,
	bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) writes:

> I have to admit that I have a problem with the different ClustalX
> versions as they do not report which ClustalW "engine" they are
> using.  I found ClustalX 1.3 uses ClustalW 1.6 etc.  You can only
> work out what is happening by checking the source code.  I mainly
> use ClustalW 1.74 as I haven't found a "ClustalX 1.74" or later.

	Well, we though about that and here is the key. The latter number is
	the good one. So, because ClustalW is stable but ClustalX still
	depends of vibrant, clustalX stays beta.
	So, ClustalX 1.64b runs ClustalW 1.74. That's all. ClustalX 1.65b is a
	platform dependant bug correction (so that is why there is no 1.65b
	for all platforms).

	...

	Well, we have to clarify it a little bit more, probably for the 2.0
	version of Clustal (both X en W) :).

> This being said I am a great admirer of ClustalX, especially
> of how portable it is.

	Many thanks to all the users who report bugs or compiled it on so much
	different platform. Also, note that it is based on the vibrant
	interface (NCBI tool kit) and NCBI people helped us a lot in tracking
	platform dependant bugs.

> THE CURE
> ========
> The cure for the problem was given by in an e-mail from Julie Thompson

	That is a team work men ! :)))). Julie is always doing the code for
	both ClustalW and ClustalX and it stays a collaboration between all
	the authors of the ClustalX paper (and all the users).

> one of the authors of ClustalW 1.7 who advised me
> 
>>can I suggest that you try setting the 'Negative matrix' option
>>in the multiple alignment parameters menu.

	I advise everyone interested in Clustal problems and workaround to
	read the october computer corner in TiBS. The answer of you question
	was in it and probably other workarounds regarding several specific
	sets of sequences.

	And hopefully, such problem reports will help us improving the Clustal
	algorithm.

		Thanks to all!
						François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France




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