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Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation

Authors:	Jessica?C?Mar Timothy?J?Harlow Email author" target="_blank">Mark?A?Ragan Email author

Institution:	(1) Department of Mathematics, The University of Queensland, 4072 Brisbane, Qld, Australia;(2) Department of Biostatistics, Harvard School of Public Health, 02115 Boston, MA, USA;(3) Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Qld, Australia;(4) Australian Research Council (ARC) Centre in Bioinformatics, Australia;(5) Program in Evolutionary Biology, Canadian Institute for Advanced Research, Canada

Abstract:	Background Bayesian phylogenetic inference holds promise as an alternative to maximum likelihood, particularly for large molecular-sequence data sets. We have investigated the performance of Bayesian inference with empirical and simulated protein-sequence data under conditions of relative branch-length differences and model violation.

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