Probability calculations of orthologous genes

by Lagervik Öster, Alice

The aim of this thesis is to formulate and implement an algorithm that calculates the probability for two genes being orthologs, given a gene tree and a species tree. To do this, reconciliations between the gene tree and the species trees are used. A birth and death process is used to model the evolution, and used to calculate the orthology probability. The birth and death parameters are approximated with a Markov Chain Monte Carlo (MCMC). A MCMC framework for probability calculations of reconciliations written by Arvestad et al. (2003) is used. Rules for orthologous reconciliations are developed and implemented to calculate the probability for the reconciliations that have two genes as orthologs. The rules where integrated with the Arvestad et al. (2003) framework, and the algorithm was then validated and tested.