how to talk homology: part 2

Jack Leunissen jackl at caos.kun.nl
Sat Nov 11 09:12:51 EST 1995

duhaimj at IRCM.UMontreal.CA (SI-Johanne Duhaime) writes:

>Thank you for all the people that answered my question about "how to talk 
>homology with pileup".  Every body suggested me to use the program 
>Distances. This give an idea about the homology between each two sets of 
>sequences of the alignment. 
>But what I am interessed in is to measure for each position of an alignment 
>a kind of score of homology. If I have 20 aligned sequences where are the 
>highlycon served regions and how much are they homologues?  This is more or 
>less the result of plotsimilary but in ascii terms.   
>Is this sound correct for "to talk homology". And is there any program 
>doing that?

No, not everybody suggested Distances. Because Distances does NOT do the
job! In my previous reply to your posting about this subject I already
suggested the use of HOMOLOGIES, which is part of the EGCG (Extended GCG)
package by Peter Rice et al. This program does everything that Distances
does, but much MORE, like calculating similarities (homologies) in stand
of distances. Moreover, the program can produce output usuable with the
PHYLIP package.

If you don't have EGCG installed on your system, this is perfect time to
have a look at it. It can be FTPed from ftp.sanger.ac.uk. It has many
important additions to the standard GCG package. And you will wonder how
you ever have been able to do without!


      Dr. Jack A.M. Leunissen. | CAOS/CAMM Center, Univ. of Nijmegen
      Email: jackl at caos.kun.nl | Toernooiveld
      Tel. : +31 24 365 22 48  | 6525 ED Nijmegen, The Netherlands
      Fax  : +31 24 365 29 77  | URL=http://www.caos.kun.nl/

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