Reconstructing phylogeny by quadratically approximated maximum likelihood.

M D Woodhams; M D Hendy

doi:10.1093/bioinformatics/bth926

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Reconstructing phylogeny by quadratically approximated maximum likelihood.

M D Woodhams·M D Hendy

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Abstract

Maximum likelihood (ML) for phylogenetic inference from sequence data remains a method of choice, but has computational limitations. In particular, it cannot be applied for a global search through all potential trees when the number of taxa is large, and hence a heuristic restriction in the search space is required. In this paper, we derive a quadratic approximation, QAML, to the likelihood function whose maximum is easily determined for a given tree. The derivation depends on Hadamard conjugation, and hence is limited to the simple symmetric models of Kimura and of Jukes and Cantor. Preliminary testing has demonstrated the accuracy of QAML is close to that of ML.

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Algorithms Chromosome Mapping Computer Simulation Evolution, Molecular Likelihood Functions Models, Genetic Models, Statistical Phylogeny Sequence Analysis, DNA Journal Article

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BibTeX RIS

M D Woodhams, M D Hendy. 2004-08-04. Reconstructing phylogeny by quadratically approximated maximum likelihood.. https://doi.org/10.1093/bioinformatics%2Fbth926

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