Software

EmpPrior: Using empirical data to inform branch-length priors for Bayesian phylogenetics

Nelson, B.J., J.J. Andersen, and J.M. Brown. 2015. Deflating trees: Improving Bayesian branch-length estimates using informed priorsSystematic 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

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 modelsSystematic Biology. 63: 289-292.

 

PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy

Brown, J.M. and R. ElDabaje. 2009. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics 25: 537-538.

 

 

Dim SumDIM SUM: Demography and Individual Migration Simulated Using a Markov chain

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.