Figure 2.

Sketch of phylogeny reconstruction from the orthologous-repeats table. (A) An orthologous-repeats table with five species and three repeats. (B) The resulting shared-repeat graph. We also illustrate the graph in matrix form. Note that the connected components of the graph correspond to clades in the final phylogeny. (C) One of the two clades has two species and is therefore resolved. The other has three species, and needs to be resolved further. (D) The orthologous-repeats subtable of species A, B, and C. Only repeat R2 contains two 1s and one 0. (E) The resulting shared-repeat subgraph resolves species A, B, and C. (F) The final phylogeny.