FIG. 3.—

An example input file for INDELible. The substitution model has been set to HKY + Γ with a transition–transversion rate ratio of κ = 2, stationary base frequencies of 0.4 (T), 0.3 (C), 0.2 (A), and 0.1 (G), and continuous gamma rate variation with shape parameter α = 1. Insertions and deletions have both been set to have an instantaneous rate of 0.1 (relative to an average substitution rate of 1) and the same geometric length distribution with a mean length of 4. Then, the phylogeny with branch lengths is specified. In the simulations for the speed tests, a 32-taxa, symmetric, strictly bifurcating tree with all branch lengths equal to 0.1 is used instead. This simulation creates 100 replicate data sets each containing one partition with a randomly created root sequence of 1,000 bases.