184 No. 91 Pupko and Pe’er Maximum Likelihood Reconstruction of Ancestral Amino-Acid Sequences

Abstract

Maximum-likelihood methods are used extensively in phylogenetic studies [3]. In particular, aminoacid sequences of ancestral species have been inferred using these methods [7]. Such ancestral reconstruction tasks aim at identifying either the most likely sequence in a specific ancestor species (marginal reconstruction), or the most likely set of ancestral states corresponding to all the ancestra

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