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Jan
2016

The quality of phylogenetic inference made from protein-coding genes depends, in part, on the realism with which the codon substitution process is modeled. Here we propose a new mechanistic model that combines the standard M0 substitution model of Yang (1997) with a simplified model from Gilchrist (2007) that includes selection on synonymous substitutions as a function of codon-specific nonsense error rates. We tested the newly proposed model by applying it to 104 protein-coding genes in brewer's yeast, and compared the fit of the new model to the standard M0 model and to the mutation-selection model of Yang and Nielsen (2008) using the AIC.
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https://theshahlab.org/pdfs/papers/Kubatko_MPE_2016.pdf
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http://www.biorxiv.org/content/biorxiv/early/2014/08/12/0078
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http://mathbio.sas.upenn.edu/premal-web/Publications_files/K
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http://linkinghub.elsevier.com/retrieve/pii/S105579031500257
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