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Subject: rate variation in ML models
Message-ID: <3432340C.3F2E at evol5.mbl.edu>
From: "Andrew J. Roger" <roger at evol5.mbl.edu>
Date: Wed, 01 Oct 1997 11:29:16 +0000
Reply-To: roger at evol5.mbl.edu
Organization: Marine Biological Laboratory
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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?
Andrew J. Roger