Fig. 2

Graphical representation of the algorithm CalculateScores-2structs. In this example, we have four species (A, B, C and D) and for each species, we have two extant RNAs (for family 1, in red, and family 2, in blue). The three major steps of the algorithm are presented. 1) The bottom-up step, where minimum scores are calculated at every node of the tree for each family. The scores take into account the substitutions, but also the basepair cost for the current family, and for the other family. 2) The middle step. Here we link the minimum score matrices for families 1 and 2 by doing a simple Fitch on the two matrices. This allows us to reconstruct the original ancestral sequences (before the duplication), taking into account both families. 3) The top-down step, where we start from the root and select the nucleotides of minimum cost at every position and construct the optimal sequences