gamma distribution/PHYLIP

Joe Felsenstein joe at
Thu Feb 29 13:19:25 EST 1996

In article <x7vikqqk5r.fsf at>,
Kent E. Holsinger <Kent at Darwin.EEB.UConn.Edu> wrote:
>>>>>> "Joe" == Joe Felsenstein <joe at>
>writes: In article <4giqf9$m06 at>
>joe at (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

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     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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