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A Bayesian approach to phylogeny reconstruction requires the
definition of a parameter space which contains the sets
of all possible combined states
where the symbol labels the possible tree
topology, are the branch lengths associated with this
topology and is a set of allowed parameters for our
evolutionary model (e.g.,
rate ratios
, nucleotide or basepair frequencies ,
gamma distribution parameter , ...). According to Bayes' theorem,
we can calculate the posterior probability of the combined state
given sequence data ,

(5) 
where is the number of possible tree topologies for a data
set containing species, is the likelihood of the data
and is the prior probability density
associated with state .
GowriShankar Vivek
20030424