Boa noite a todos,

Teremos amanhã, 4 de Dezembro, quarta-feira, pelas 16:00, na sala V1.08,
Pavilhão de Civil, IST Alameda, a apresentação e discussão da tese de mestrado
da Mariana Costa, "Simulation based approach to bacterial evolution".

Resumo: The aim of this study is firstly to provide scientific background
relating to phylogenetic tracking of bacterial genome through existing models
that simulate the effective behavior, serving as source of assessing how to
infer the true population structure. Understanding bacterial population
genetics and evolution is key in epidemic outbreak studies and surveillance of
infectious diseases. Current literature focuses on several theories and
mathematical models regarding this issue, namely the Wright-Fisher model, the
Infinite alleles model and the Coalescent model. A practical application is
also studied by means of SimBac, a simulation software.  Taking this into
consideration, the question lies on whether it is possible to accurately
portrait the relationship between a given sample of individuals taken from the
population, via phylogenetic inference algorithms. In this manner, we will
focus our analysis on UPGMA, Neighbor-Joining, goeBURST Full MST, GrapeTree
and two Bayesian approaches, BAPS and ClonalFrame. Of course, all of them
yield different graph structures and therefore, the need to compare graphs has
risen and several metrics were established and researched, such as the
Robinson Foulds distance. The theoretical analysis exposed in the first
sections supports practical applicability, such as the implementation of an
algorithm that simulates bacterial behavior and several experiments that are
evaluated in an attempt of concluding on the ability of phylogenetic
algorithms when applied in diverse situations that simulate a real
environment.

Saudações,

Alexandre Francisco