Fig. 3

SISRS produced substantial amounts of informative data for phylogenies of different shapes and evolutionary distances. The number of true variable sites identified from simulated data is shown for each of the six simulation trees (symbols; Fig. 2) for increasing numbers of substitutions between species (panels; increasing values of t), and increasing levels of coverage (x axis). Symbols are ∘ for balanced trees; △ for balanced trees with long deep branches; ■ for balanced trees with short deep branches; \(\blacktriangle \) for ladder trees; ∗ for ladder trees with long deep branches; ∙ for ladder trees with short deep branches. These sites were identified from 1 million base pair genomes; thus, larger genomes are expected to produce more sites, particularly as long as a fraction of those genomes are reasonably conserved