Estimating clock-like branch lengths
strimmer at zi.biologie.uni-muenchen.de
Fri Jan 12 07:04:43 EST 1996
Given a possibly multifurcating tree T, a model of sequence evolution M,
and the data set D (nucleotides or amino acids), how can I assign branch
lengths to T in such a way that T obeys a molecular clock?
The preferred way is, of course, maximum likelihood. If T is strictly
bifurcating, if the data are nucleotides, and if the model of sequence
evolution is the F84 model, I use maximum likelihood as implemented in
Which programs are available if T is multifurcating? Or if D are amino acids?
(NucML or ProtML provide many models and can be applied to multifurcating trees,
but they don't return a clock-like tree ... !)
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