In article <6as9hl$2f4$1 at lyra.csx.cam.ac.uk>,
tjrc1 at mole.bio.cam.ac.uk (Tim Cutts) writes:
> Some users of mine have found that GCG MSF files as output by clustalw
> 1.74 do not work well with pretty from GCG 9.1. This is because the
> weight values output by clustalw are very small. Thus I have created
> this tiny patch to clustalw 1.74 to scale up all the weights it
> outputs in GCG files by a factor of 100. Works for me! If anyone can
> think of any problems this might cause I'd like to hear them.
Well, perhaps would be better to patch pretty ;-).
The weights given by ClustalW are the weights used for
the weighted profile calculation during the multiple alignment
process. We feel useful for the user to know what were the weights
used.
Also, it's just a patch on an output format option, I
would like to see a printf("weight scaled for pretty compatibility\n").
with a scale factor indicated here...
And yes, the new licence of GCG does not permit very
easily fixes on GCG programs, but is it a good reason to submitt
a patch on our program? Nothing was possible on the GCG side?
Anyway, we will apply your changes to the following version
of Clustal, and document it a little bit.
François.
--
François Jeanmougin | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
