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Pairwise identity from multiple alignment with DISTANCES

David Mathog mathog at seqvax.caltech.edu
Wed Dec 21 13:40:00 EST 1994


In article <1994Dec20.155439.171654 at eros.embl-heidelberg.de>, ouzounis at embl-heidelberg.de (Christos Ouzounis) writes...
>In article <3ct5dk$psr at mserv1.dl.ac.uk>, jackl at camms1.caos.kun.nl (Jack Leunissen) writes:
>> 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. 

$ sho sym *dist*
  DIST*ANCES == "$GENUTIL:DISTANCES"
  OLDDIST*ANCES == "$GENUTIL:OLDDISTANCES"

OLDDISTANCES, is (big surprise) the old Distances program.  

We had the exact same problem a month or two ago.  No, I didn't find it
either, but help at gcg.com supplied this nugget of information.

Regards,

David Mathog
mathog at seqvax.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 



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