An analysis of models and algorithms for gene duplication and lateral gene transfer /

The construction of phylogenetic trees commonly uses molecular sequence data (DNA, RNA or amino acid sequences) for a single gene family over a set of n extant taxa. However, difficulties arise when the phylogenetic gene tree for one gene family disagrees with the phylogenetic gene tree for a different gene family. Several computational problems arise when trying to explain this disagreement (the two gene trees are not equal). Typically, one assumes a (simplified) model of evolution restricted to a small set of events which are assumed to cause the disagreement. Two such well-studied events are gene duplications and lateral gene transfer (a.k.a. horizontal gene transfer).This thesis explores several aspects of both of these simplifed models of evolution. A brief exposition of the models is presented, along with previous results and various extensions to these models.The expected number of gene duplications needed to explain disagreements between a random gene and species tree is investigated.A method for incorporating edge weights into the species tree is proposed