Phylogenetic estimation with partial likelihood tensors

JOURNAL OF THEORETICAL BIOLOGY

卷:262

Article

Sumner, J. G.^1,2  Charleston, M. A.^2,3 

[1] Univ Tasmania, Sch Math & Phys, Hobart, Tas 7001, Australia

[2] Univ Sydney, Sch Informat Technol, Sydney, NSW 2006, Australia

[3] Univ Sydney, Ctr Math Biol, Sydney, NSW 2006, Australia

关键词: Phylogenetics;    Maximum likelihood;    Computational complexity;    Tensors;   

DOI  :  10.1016/j.jtbi.2009.09.037

来源: Elsevier

【 摘 要 】

We present an alternative method for calculating likelihoods in molecular phylogenetics. Our method is based on partial likelihood tensors, which are generalizations of partial likelihood vectors, as used in Felsenstein's approach. Exploiting a lexicographic sorting and partial likelihood tensors, it is possible to obtain significant computational savings. We show this on a range of simulated data by enumerating all numerical calculations that are required by our method and the standard approach. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.

【 授权许可】

Free