Computational Advances in Maximum Likelihood Methods for Molecular Phylogeny

Maximum Likelihood Methods in Molecular Phylogenetics

DPRml: distributed phylogeny reconstruction by maximum likelihood

MOTIVATION In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximu...

Fast Parallel Maximum Likelihood-Based Protein Phylogeny

Inferring phylogenetic relationships between sequences is a difficult and interesting problem. Assuming that there is enough phylogenetic signal in biological sequence to resolve every tree bifurcation, the resulting tree is a representation of the vertical descent history of a gene. A popular method to evaluate a candidate phylogenetic tree uses the likelihood of the data, given an empirical m...

Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood

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 fun...

Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference

Accurate phylogenies are critical to taxonomy as well as studies of speciation processes and other evolutionary patterns. Accurate branch lengths in phylogenies are critical for dating and rate measurements. Such accuracy may be jeopardized by unacknowledged sequencing error. We use simulated data to test a correction for DNA sequencing error in maximum likelihood phylogeny inference. Over a wi...