Improving the Study of Gene Rearrangement in Bayesian Phylogeny
McAnulty College and Graduate School of Liberal Arts
Donald L. Simon
Kathleen A. Taylor
Bayesian Phylogeny, Markov chain Monte Carlo, Three Neighbors of an Internal Node
Examining gene rearrangement is one important method for constructing phylogenies, or evolutionary histories, of taxa. Our research uses Bayesian approach, implemented by a Markov chain Monte Carlo algorithm, for finding the most probable phylogenies and assessing their likelihood given gene arrangement data. In past research, when updating trees, algorithms examined the arrangement data stored in pairs of connected nodes. We develop a new method, which examines the arrangements of the three neighbors of an internal node. The rearrangements found by the method are not guaranteed to be optimal, but will, with high probability, be close to optimal. Initial tests show that the new update method improves the MCMC procedure.
Yang, X. (2004). Improving the Study of Gene Rearrangement in Bayesian Phylogeny (Master's thesis, Duquesne University). Retrieved from https://dsc.duq.edu/etd/1616