Figure 3

Optimized Sankoff parsimony: up phase. (A) Cost matrix between six states a, ..., f and their associated cost tree as calculated by the neighbor-joining algorithm. (B) A simple phylogeny with three nodes (dashed boxes), their cost vectors S and cost trees T _C . Cost vectors S^(q)and S^(r), and cost trees $T_C^{(q)}$ and $T_C^{(r)}$ are already calculated. (C) Step-by-step reconstruction of S^(p)and $T_C^{(q)}$ for node p following Algorithm 3.