Algorithms to Reconstruct Evolutionary Events at Molecular Level and Infer Species Phylogeny
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Mathematical methods and models for comparative analysis of large sets of protein phylogenies are described. The processes modeled are gene duplication, loss, gain, and horizontal transfer. Initially, a species tree is constructed as a consensus of the corresponding gene trees using probabilistic distribution on source data. Algorithms are further implemented to identify vertices accounting for topological disparities between the gene and species trees, with possibility to infer underlying evolutionary events. The analysis is illustrated on case studies of a prokaryotic protein family and a set of protein phylogenies deduced from families from the COGs database (NCBI). The potential of the described methods to infer phylogeny and gene evolution events is discussed.
Key wordsevolution phylogenetic tree consensus tree gene duplication gene loss horizontal gene transfer mathematic models of evolution stochastic optimization
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