Nelson, B.J., J.J. Andersen, and J.M. Brown. 2015. Deflating trees: Improving Bayesian branch-length estimates using informed priors. Systematic Biology. 64:441-447.
Andersen, J.J., B.J. Nelson, and J.M. Brown. 2016. EmpPrior: Using empirical data to inform branch-length priors for Bayesian phylogenetics. In Review.
AMP: Analysis of Model adequacy using Posterior predictive simulation
Brown, J.M. 2014. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. Systematic Biology. 63: 334-348.
See also: Brown, J.M. 2014. Predictive approaches to assessing the fit of evolutionary models. Systematic Biology. 63: 289-292.
Brown, J.M. and R. ElDabaje. 2009. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics 25: 537-538.
Brown, J.M., K. Savidge, and E. McTavish. 2010. DIM SUM: Demography and individual migration simulated using a Markov chain. Molecular Ecology Resources 11: 358-363.
Scripts and other useful things
molecular-biology-and-evolution2.csl: Corrected Mendeley citation style file for Molecular Biology and Evolution. The use of journal abbreviations also requires an additional file (default.txt) to link full and abbreviated names. Directions for using journal abbreviations can be found here. Created by Vinson Doyle.
transferBranchLabels.py: This is a relatively simple python script (using the Dendropy library) to transfer branch-specific labels between trees (which can differ in topology). Some information on program execution can be found in this blog post or by running the program with a --help flag (e.g., python transferBranchLabels.py --help).
Other assorted code available on Jeremy's GitHub page.