Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

• Published in: Philosophical transactions of the Royal Society of London. Series B. Biological sciences Vol. 363; no. 1512; pp. 3977 - 3984
• Main Authors: Stamatakis, Alexandros, Ott, Michael
• Format: Journal Article
• Language: English
• Published: London The Royal Society 27.12.2008
• Subjects: Algorithms; Architecture; Branches; Computational Biology - methods; Computer architecture; Computer Simulation; Data models; Datasets; Genetic vectors; Likelihood Functions; Mathematical vectors; Maximum Likelihood; Multi-Core Architectures; Multi-Gene Phylogenies; OpenMP; Phylogenetic Inference; Phylogenetics; Phylogeny; Plant roots; RAxML; Sequence Alignment - methods; Topology

The continuous accumulation of sequence data, for example, due to novel wet-laboratory techniques such as pyrosequencing, coupled with the increasing popularity of multi-gene phylogenies and emerging multi-core processor architectures that face problems of cache congestion, poses new challenges with...