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Gibbs sampler for statistical multiple alignment

by Jens Ledet Jensen and Jotun Hein
Research Reports Number 429 (September 2002)
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.
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