Stephane Vuilleumier wrote:
> I previously used DISTANCES with parameter set to 1.5 to calculate
> pairwise identities between sequences in a multiple alignment. In the
> new GCG version now installed at our site, this possibility has (as far as I
> can tell) disappeared (choice between uncorrected, Jukes-Cantor and
> Kimura distances), and the output is the number of substitutions per
> 100 nucleotides.
> Can I still use GCG to do pairwise identities from a MSF alignment in
> this version of the program?
You're probably referring to the extended version of DISTANCES, called
HOMOLOGIES (yes, I know, very imaginative) that can be used to calcul-
ate both similarities or distances, augmented distances (Jukes-Cantor,
Kimura), and produce PHYLIP input files. This program will be part of
the EGCG (Extended GCG) distribution which is currently being produced
by Peter Rice (EBI) et al.
Don't dispair; coming soon...!
Cheers,
Jack
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Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center
Email: jackl at caos.kun.nl | University of Nijmegen
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