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Probabilistic ancestral sequence.

A probabilistic ancestral sequence (PAS) is like a protein sequence where each position, instead of an amino acid, has a vector of dimension $\vert\Sigma\vert$ describing the probability of each amino acid being in that position. A PAS is normally associated to an EPT and to a particular place in this tree. It is normally most interesting to compute the PAS at divergence points or at the root of the EPT. E.g. find the PAS for the common ancestor of all mammals.

Gaston Gonnet