Summary of the multiple sequence alignment simulation experiments that were performed in this study using different branch length distributions, substitution models and tree topologies.

U(min, max) = uniform distribution with the corresponding minimum and maximum parameter values. Exp(α) = exponential distribution with the corresponding mean parameter α. ϵ is the relative extinction parameter for the birth-death model (i.e. μ/λ where μ and λ are the death and birth parameters, respectively) and a is the age of the root node in Mya of the birth-death model. BL-space = branch-length heterogeneity space. Each simulation consists of a combination of a specific branch length distribution, substitution model and tree topology. For example, the “exponential” experiment includes a total of six parameter combinations: all pairs of the three branch length distributions and two substitution models in the “Exponential” entry in the table.