J. Comput. Biol. - Maximum parsimony, substitution model, and probability phylogenetic trees.

Tópicos

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Resumo

The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

Resumo Limpo

problem infer phylogeni phylogenet tree one main problem comput biolog three main method infer phylogeniesmaximum parsimoni mp distanc matrix dm maximum likelihood ml mp method wellstudi popular method mp method optim criterion number substitut nucleotid comput differ investig nucleotid sequenc howev mp method often critic count substitut observ current time unobserv substitut realli occur evolutionari histori omit order take account unobserv substitut substitut model establish now wide use dm ml method substitut model use within classic mp method recent author propos probabl represent model phylogenet tree reconstruct tree model call probabl phylogenet tree one advantag probabl represent model can includ substitut model infer phylogenet tree base mp principl paper explain use substitut model reconstruct probabl phylogenet tree show advantag approach exampl

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