Figure 1

Overview of the π BUSS simulation procedures and GUI screenshot. A. Schematic representation of the different ways to employ the πBUSS simulation software. Based on an XML input file, simulations can be performed using the core implementation. BEAST can parse the specified πBUSS instructions and generate sequence data as well as analyze the replicate data in a single run. Using both the GUI or CLI, πBUSS can run simulations based on an input tree or a list of taxa and their heights. The software can also write the simulation settings to an XML file that can be then read by BEAST. B. The screenshot example shows the set-up of a codon position partitioned simulation in the Partitions panel of the graphical user interface. The Hasegawa, Kishino and Yano (HKY) model is being set as the substitution model for partition 1, with a κ (the transition-transversion bias) parameter value of 4.0.