Program Flow. The diagram indicates the simulation program flow used to construct the supermatrix, our simulated CGH data matrix. Variables that can be modified include the number of sequences input, the topology of the tree used, and the amount of divergence among taxa in the simulated alignment, and the choice of evolutionary model to evolve and calculate genetic distance among taxa (see methods). Neighbor-Joining (NJ) and Parsimony Majority-Rule (PMR) trees were constructed from the supermatrix.
Gilbert et al. BMC Genomics 2011 12:456 doi:10.1186/1471-2164-12-456