Fig 1. A species tree S and a multifurcated gene tree G.
Each leaf xi or x of G represents a gene belonging to genome x present as a leaf in S. Step (1) of ProfileNJ is PolytomySolver, which resolves each polytomy P of G independently. A dynamic programming table M is constructed. Step (2) of ProfileNJ takes as input a count vector V, here resulting from the backtracking path related by rectangles and arrows in table M, and a distance matrix d for the considered genes. A Neighbor joining (NJ) based procedure computes the gene tree in agreement with V that best reflects the distance matrix. The final completely refined tree is given bottom right. Duplication nodes are indicated by squares.