Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.
Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11-222, Palmerston North, New Zealand
Received on January 15, 2004; accepted on March 1, 2004
Summary: 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.
Contact: m.d.woodhams{at}massey.ac.nz