Implementation and investigation of codon and amino acid models in maximum likelihood phylogenetic software (Visiting Scholar)
Molecular phylogenetics involves the inference of the evolutionary relationships between organisms based on biological data such as DNA sequences. Knowledge of these historical relationships (usually represented as a phylogenetic tree) is useful in fields such as medicine, epidemiology and conservation, among others. These inferred relationships are thought to be most accurate when detailed knowledge about the evolutionary processes affecting the sequences is utilized. Many ways of modeling these processes have been previously investigated, but some of the most realistic have not been because of their large computational burden. My project focuses on the implementation and investigation of a particular type of complex evolutionary model that takes into account the genetic code and is based on codons or DNA triplets.