2,044 research outputs found
EM for phylogenetic topology reconstruction on non-homogeneous data
Background: The reconstruction of the phylogenetic tree topology of four taxa
is, still nowadays, one of the main challenges in phylogenetics. Its
difficulties lie in considering not too restrictive evolutionary models, and
correctly dealing with the long-branch attraction problem. The correct
reconstruction of 4-taxon trees is crucial for making quartet-based methods
work and being able to recover large phylogenies.
Results: In this paper we consider an expectation-maximization method for
maximizing the likelihood of (time nonhomogeneous) evolutionary Markov models
on trees. We study its success on reconstructing 4-taxon topologies and its
performance as input method in quartet-based phylogenetic reconstruction
methods such as QFIT and QuartetSuite. Our results show that the method
proposed here outperforms neighbor-joining and the usual (time-homogeneous
continuous-time) maximum likelihood methods on 4-leaved trees with
among-lineage instantaneous rate heterogeneity, and perform similarly to usual
continuous-time maximum-likelihood when data satisfies the assumptions of both
methods.
Conclusions: The method presented in this paper is well suited for
reconstructing the topology of any number of taxa via quartet-based methods and
is highly accurate, specially regarding largely divergent trees and time
nonhomogeneous data.Comment: 1 main file: 6 Figures and 2 Tables. 1 Additional file with 2 Figures
and 2 Tables. To appear in "BCM Evolutionary Biology
Quartet consistency count method for reconstructing phylogenetic trees
Among the distance based algorithms in phylogenetic tree reconstruction, the
neighbor-joining algorithm has been a widely used and effective method. We
propose a new algorithm which counts the number of consistent quartets for
cherry picking with tie breaking. We show that the success rate of the new
algorithm is almost equal to that of neighbor-joining. This gives an
explanation of the qualitative nature of neighbor-joining and that of
dissimilarity maps from DNA sequence data. Moreover, the new algorithm always
reconstructs correct trees from quartet consistent dissimilarity maps.Comment: 11 pages, 5 figure
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