How to talk homology with pileup

Akemi Yagi yagi2 at scripps.edu
Wed Nov 8 11:03:59 EST 1995

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

|Let's say that you do a pileup with a set of sequences.  How to talk 
|homology with the result? Let me make that clearer. With the program gap 
|you can say: in that segment of the two sequences you have xx% of 
|similarity. But with pileup you do not have such a result.  You can use 
|Plotsimilary to have an idea of the similarity but it is a graphical 
|Do you have any suggestion on that. When you publish how do you point 
|out the similarity?

The program you might want to look at is "distances" which writes a table
of the pairwise distances between aligned sequenses.  If you are running
Version 8, try also the "olddistances" program.

Akemi Yagi
yagi2 at scripps.edu

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