gamma distribution/PHYLIP

Kent E. Holsinger kent at darwin.darwin.eeb.uconn.edu
Thu Feb 29 09:30:08 EST 1996

>>>>> "Joe" == Joe Felsenstein <joe at evolution.genetics.washington.edu>
writes: In article <4giqf9$m06 at nntp3.u.washington.edu>
joe at evolution.genetics.washington.edu (Joe Felsenstein) writes:

    Joe> In likelihood methods (such as Ziheng Yang's methods that use
    Joe> gamma-distributed rates in his PAML package, or my Hidden
    Joe> Markov Model approach in DNAML) one can change the rate
    Joe> variation parameters until the overall likelihood of the tree
    Joe> is maximized.  With distance methods, I am not as sure how to
    Joe> do this.  Perhaps one could try various values until the
    Joe> goodness of fit of the tree (say, the sum of squares) is
    Joe> optimized, but doing this may have biases in it.

I don't think comparing goodness-of-fit values would work, unless they
were normalized in some way. The distance between sequences A and B
increases as the coefficient of variation increases, so the total tree
length would also increase as the coefficient of variation
increases. It's not obvious to me that there is a scale-invariant way
of comparing the goodness-of-fit statistics, but maybe I'm missing
something. (It wouldn't be the first time.)

-- Kent

Kent E. Holsinger                Kent at Darwin.EEB.UConn.Edu
-- Department of Ecology & Evolutionary Biology          
-- University of Connecticut, U-43                                       
-- Storrs, CT   06269-3043                                               

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