Ron Kagan rkagan at
Mon Jan 22 19:08:43 EST 1996

I have a question for any of you who are familiar with the use of maximum
likelihood analysis in Felsenstein's PHYLIP package:  How should I set
the "categories" option for defining how many categories of substitution
sites there are and the relative rates for each?  I'm doing a DNAML and
DNAMLK analysis of coding regions, so I was thinking that there should be
2 categories of rates, one for the synonymous substitutions and one for
the non-synonymous substitutions.  An average value for this ratio (for
42 genes, Nei, 1987, p.80) is about 5.3:1.  Should I use this ratio, or
should I empirically determine what it is for my sequences.  If I decide
to determine this, what program might I use?


Ron Kagan

"If you love wealth better than liberty, the tranquility of servitude
better than the animating contest of freedom, go home from us in peace. 
We ask not your counsels or arms.  Crouch down and lick the hands which
feed you.  May your chains set lightly upon you, and may posterity forget
that ye were our countrymen." 

                        - Samuel Adams, 1776
Ron Kagan, Ph.D.
Dept. of Chemistry and Biochemistry, UCLA
rkagan at

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