10. Citing PyMsBayes

If you publish results obtained using this software, please cite the software and the appropriate citations for the bundled tools that were used:

• dpp-msbayes and euReject: [8]
• msBayes: [6]
• ABCtoolbox: [12]

11. Literature Cited

[1]	Mark Beaumont, Wenyang Zhang, and David J. Balding. Approximate Bayesian computation in population genetics. Genetics, 162:2025–2035, 2002.

[2]	E. T. Bell. Exponential numbers. American Mathematical Monthly, 41:411–419, 1934.

[3]	Thomas S Ferguson. A Bayesian Analysis of Some Nonparametric Problems. The Annals of Statistics, 1(2):209–230, March 1973.

[4]	Masami Hasegawa, Hirohisa Kishino, and Taka-aki Yano. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22(2):160–174, 1985.

[5]

Michael J. Hickerson, Graham N. Stone, Konrad Lohse, Terrence. C. Demos, Xiaoou Xie, Cedric Landerer, and Naoki Takebayashi. Recommendations for using msbayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al. Evolution, 68(1):284–294, 2014. URL: http://doi.wiley.com/10.1111/evo.12241, doi:10.1111/evo.12241.

[6]	Wen Huang, Naoki Takebayashi, Yan Qi, and Michael J. Hickerson. MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. BMC Bioinformatics, 12:1, 2011. doi:10.1186/1471-2105-12-1.

[7]	Christoph Leuenberger and Daniel Wegmann. Bayesian computation and model selection without likelihoods. Genetics, 184:243–252, 2010. doi:10.1534/genetics.109.109058.

[8]	Jamie R. Oaks. An improved approximate-bayesian model-choice method for estimating shared evolutionary history. arXiv:1402.6303 [q-bio.PE], ():, 2014. URL: http://arxiv.org/abs/1402.6303, doi:.

[9]	Jamie R. Oaks, Charles W. Linkem, and Jeet Sukumaran. Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: a reply to hickerson et al. arXiv:1402.6397 [q-bio.PE], ():, 2014. URL: http://arxiv.org/abs/1402.6397, doi:.

[10]

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron D. Siler, Mark T. Holder, and Rafe M. Brown. Evidence for climate-driven diversification? a caution for interpreting ABC inferences of simultaneous historical events. Evolution, 67(4):991–1010, 2013. doi:doi:10.1111/j.1558-5646.2012.01840.x.

[11]	Christian P Robert, Jean-Marie Cornuet, Jean-Michel Marin, and Natesh S Pillai. Lack of confidence in approximate Bayesian computation model choice. Proceedings of the National Academy of Sciences, 108(37):15112–15117, September 2011.

[12]	Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander, and Laurent Excoffier. ABCtoolbox: a versatile toolkit for approximate bayesian computations. BMC Bioinformatics, 11:116, 2010. doi:10.1186/1471-2105-11-116.