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Summary: The Posterior Probability Distribution of Alignments
and its Application to Parameter Estimation of Evolutionary Trees
and to Optimisation of Multiple Alignments.
L. Allison * & C. S. Wallace
TECHNICAL REPORT NO: 93/188
July 1993
email: lloyd@cs.monash.edu.au
Partly supported by Australian Research Council grant A49030439
* to whom correspondence should be sent.
Abstract. It is shown how to sample alignments from their posterior probability distribution given two
strings. This can be extended to alignments of alignments. The result is firstly applied to the estimation of
the edges of a given evolutionary tree over several strings. Secondly, when used in conjunction with
simulated annealing, it gives a stochastic search method for an optimal multiple alignment.
Keywords: alignment, estimation, evolutionary tree, inductive inference, multiple alignment, sampling,
stochastic.
LA Computer Science, Monash University TR 93/188 1993
Posterior Probability Distribution of Alignments 2
1. Introduction.
Estimating the evolutionary "distance" between some given strings, for example DNA sequences, and
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