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.