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.

<p>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.</p>

This research investigates existing relationships between the three apparently unrelated subjects: Markov process, Semigroups and Partial difierential equations. Markov processes define semigroups through their transition functions. Conversely particular semigroups determine transition functions and can be regarded as Markov processes. We have exploited these relationships to study some Markov chains. The infnitesimal generator of a Feller semigroup on the closure of a bounded domain of Rn; (n ^ 2), is an integro-diferential operator in the interior of the domain and verifes a boundary condition. The existence of a Feller semigroup defined by a diferential operator and a boundary condition is due to the existence of solution of a bounded value problem. From this result other existence suficient conditions on the existence of Feller semigroups have been obtained and we have applied some of them to construct Feller semigroups on the unity disk of R2. / Decision Sciences / M. Sc. (Operations Research)

This research investigates existing relationships between the three apparently unrelated subjects: Markov process, Semigroups and Partial difierential equations. Markov processes define semigroups through their transition functions. Conversely particular semigroups determine transition functions and can be regarded as Markov processes. We have exploited these relationships to study some Markov chains. The infnitesimal generator of a Feller semigroup on the closure of a bounded domain of Rn; (n ^ 2), is an integro-diferential operator in the interior of the domain and verifes a boundary condition. The existence of a Feller semigroup defined by a diferential operator and a boundary condition is due to the existence of solution of a bounded value problem. From this result other existence suficient conditions on the existence of Feller semigroups have been obtained and we have applied some of them to construct Feller semigroups on the unity disk of R2. / Decision Sciences / M. Sc. (Operations Research)

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