Ancestral sequences

Ancestral sequences are inferred from the EPO multiple alignments using Ortheus. Ortheus is a probabilistic method for the inference of ancestor, a.k.a tree, alignments. The main contribution of Ortheus is the use of a phylogenetic model incorporating gaps to infer insertion and deletion events. Ancestral sequences are predicted for each node of the phylogenetic tree that relates the sequences. Each ancestral sequence is named according to the derived extant species. For example, a sequence named "((homo_sapiens,pan_troglodytes),macaca_mulatta)" corresponds to the ancestor of the Homo sapiens, Pan troglodytes, and Macaca mulatta genomes.