rate variation in ML models

newsmgr at merrimack.edu newsmgr at merrimack.edu
Wed Oct 1 13:03:49 EST 1997


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Subject: rate variation in ML models
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From: "Andrew J. Roger" <roger at evol5.mbl.edu>
Date: Wed, 01 Oct 1997 11:29:16 +0000
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Hi,

sorry for this naive question. I was wondering how the discrete gamma
distribution is factored into likelihood calculations.  

Are particular sites assigned a rate category in advance OR
does every site have a certain probability of being in one
of the rate classes (thus the calculations for each rate category
are done for each site and summed over the whole lot- low
probability assignments then contribute little to the overall
probability, and high probability assignments contribute
a lot to the overall probability).

Are all among-site-rate-variation models incorporated into
the calculations the same way?

Finally, does the way that one deal with this problem affect
whether or not the i.i.d. assumption holds for a dataset?

Cheers
Andrew J. Roger




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