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Invariable sites question

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Nov 25 14:16:05 EST 1996

In article <Pine.A32.3.95.961125154742.16153A-100000 at wap18.zi.biologie.uni-muenchen.de>,
Korbinian Strimmer  <strimmer at zi.biologie.uni-muenchen.de> wrote:
[In response to an inquiry by James McInerney]
>Finally, I'd like to mention the practcal problem: though the
>ML method with invariable sites is old (1985) I don't know
>how to do it in practise with any published program (please
>tell me if you know such a ML estimation program!)
>In the ML program that Arndt and I am developing we will
>incorporate such an estimator but as there are also other
>features in the works it'll take some time until we'll give
>it away. (If you like, there is a prliminary test version that
>can estimate f but don't rely to much on it because it still
>is very buggy:

In DNAML in PHYLIP version 3.5, we have a Hidden Markov Model computational
scheme.  All you need to do is tell it there are two (or more) categories of
site, one of which has rate 0.  You then get an estimate of the tree, with
likelihood.  The prior probability of the 0-rate category that you are asked
to supply is the quantity f that you have been talking about.  It is not
inferred by DNAML -- you have to do a number of runs with different f's
and ask which has the highest likelihood.

That aside, it does what you need.  Note that it does not involve anyone
specifying which are the sites that are invariable.

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

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