Marcelo Serrano Zanetti

Building Phylogenetic Trees: Maximum Likelihood Methods Based on Markovian Codon Models of Molecular Evolution Marcelo Serrano Zanetti

This book introduces Markovian codon models of evolution in maximum likelihood phylogeny inference. The literature show that codon models constitute a more realistic representation of protein-coding sequences when compared against amino acid and nucleotide models. Our results extend this by showing that codon models are also expected to outperform these two competing approaches when re-constructing phylogenetic trees. To enable this analysis, we have created a software package called CodonPhyml, which is freely available under an open source license.