Can somebody explain to me how exactly to chose the right substitution model in BEAST? I understand there are some modelling softwares that suggest the most appropriate model. But what in general determines the model?
Bayesian information criterion (BIC) and decision theory (DT) should be preferred
for model selection. Together with model-adequacy tests, accurate model selection will serve to improve the reliability of phylogenetic inference and related analyses
Reference:
Luo A, Qiao H, Zhang Y, Shi W, Ho S Y, Xu W, Zhang A, Zhu C. Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol, 2010, 10: 242.
Thanks Gao, what would determine the Molecular Clock Rate? Strict, Relax, Estimate?
There is no direct answer to go for Strict or relax. You can refer to the previously published paper and adopt the same. Or do all combination of available models, compare and choose the best fit model.
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