Reconstruction of Ancestral Sequences by the Inferential Method, a Tool for Protein Engineering Studies

The paper describes the inferential method, an approach for reconstruction protein and nucleotide sequences of ancestral species starting from known, homologous, contemporary sequences. The method is tested by computer simulation of speciation and nucleotide substitutions stating from a single ancestral sequence and subsequent reconstruction of nodal sequences. Good agreement of the results has been obtained by comparing protein sequence reconstructions carried out with the inferential method with those obtained using the maximum parsimony method in two different cases.