View article

Computer simulations are useful because they can characterize the expected performance of phylogenetic methods under idealized conditions. However, simulation studies are also subject to several sources of bias that make the results of different simulation studies difficult to interpret and often contradictory. In this study, I examined the performance of 26 commonly used methods of phylogenetic inference for three statistical criteria: consistency, efficiency, and robustness. Methods examined included parsimony (general, weighted, and transversion), maximum likelihood (assuming Jukes-Cantor and Kimura models of DNA substitution), and UPGMA, minimum evolution, and weighted and unweighted least squares (with uncorrected, Jukes-Cantor, Kimura, modified Kimura, and gamma distances). The performance of methods was examined under three models of DNA substitution for four taxa. The branch …