gamma distribution/PHYLIP

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Feb 29 13:19:25 EST 1996


In article <x7vikqqk5r.fsf at darwin.darwin.eeb.uconn.edu>,
Kent E. Holsinger <Kent at Darwin.EEB.UConn.Edu> wrote:
>>>>>> "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.

I agree for the distance measures, and that was why I was worried about
biases in going this for them.  But for maximum likelihood methods it
works well, and has no known problems.

-- 
Joe Felsenstein         joe at genetics.washington.edu     (IP No. 128.95.12.41)
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA



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