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Pairwise identity from multiple alignment with DISTANCES

Jack Leunissen jackl at camms1.caos.kun.nl
Fri Dec 16 17:47:16 EST 1994


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

    +----------------------------------------------------------------+
      Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center
      Email: jackl at caos.kun.nl   | University of Nijmegen
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