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\noindent Statistica Sinica {\bf 15}(2005), 889-907

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\centerline{\large\bf GIBBS SAMPLER FOR STATISTICAL MULTIPLE}
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\centerline{\large\bf  ALIGNMENT}
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\author{Jens Ledet Jensen and Jotun Hein}
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\centerline{\it University of Aarhus and Oxford University}
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\begin{quotation}
\noindent {\it Abstract:}
For a set of sequences, related by a binary tree, that have
evolved according to the Thorne-Kishino-Felsenstein model, a Gibbs
sampler is presented for simulating the ancestral sequences and
their alignments. The updating step consists in updating the
ancestral sequence and its three alignments within a 3-star tree.
We compare the Gibbs sampler with the algorithm suggested recently
by Holmes and Bruno.\par
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\noindent {\it Key words and phrases:}
3-star tree, EM-algorithm, evolutionary model,
hidden Markov model, Markov chain Monte Carlo.
\par
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