PAUP-distances

[Mark Siddall]

In article <Pine.SUN.3.91.950221085814.1297B-100000 at unixg.ubc.ca> dion at UNIXG.UBC.CA (Dion G Durnford) writes:
>
>	I was wondering if anyone new what formula PAUP uses to calculate 
>the distance matrix and how gaps are treated.  I want to use it just to 
>get a rough idea of %identity at the amino acid level of a number of 
>proteins. I can't seem to find this information anywhere,