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A Branch-and-Bound Algorithm for the Inference of Ancestral Amino-Acid Sequences When the Replacement Rate Varies among Sites

By Tal Pupko, Itsik Pe&apos, Masami Hasegawa, Dan Graur and Nir Friedman


Motivation: We developed an algorithm to reconstruct ancestral sequences, taking into account the rate variation among sites of the protein sequences. Our algorithm maximizes the joint probability of the ancestral sequences, assuming that the rate is gamma distributed among sites. Our algorithm provably finds the global maximum. The use of joint reconstruction is motivated by studies that use the sequences at all the internal nodes in a phylogenetic tree, such as, for instance, the inference of patterns of amino-acid replacements, or tracing the biochemical changes that occurred during the evolution of a protein along a predefined lineage

Year: 2007
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