Anc-gene is a software for inference of ancestral nucleotide sequences of protein coding genes from a set of present-day sequences whose phylogenetic relationships are known. It first infers the amino acids by the distance-based Bayesian method, and then infers the underlying nucleotide sequences by fixing the inferred amino acids.
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Zhang J, Rosenberg HF, Nei M (1998)
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
Proc. Natl. Acad. Sci. USA 95:3708-3713.