MBE Advance Access originally published online on October 19, 2006
Molecular Biology and Evolution 2007 24(1):288-293; doi:10.1093/molbev/msl153
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Research Articles |
Performance of a New Invariants Method on Homogeneous and Nonhomogeneous Quartet Trees
Department of Matemàtica Aplicada I, Universitat Politècnica de Catalunya, Barcelona, Spain
E-mail: marta.casanellas{at}upc.edu.
Accepted for publication October 17, 2006.
An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several researchers (the initial idea due to Lake [1987] and Cavender and Felsenstein [1987]). However, the efficiency of methods based on invariants is still in doubt (Huelsenbeck 1995; Jin and Nei 1990). Probably because these methods only used few generators of the set of phylogenetic invariants. The method studied in this paper was first introduced in Casanellas et al. (2005) and it is the first method based on invariants that uses the "whole" set of generators for DNA data. The simulation studies performed in this paper prove that it is a very competitive and highly efficient phylogenetic reconstruction method, especially for nonhomogeneous models on phylogenetic trees.
Key Words: invariants • phylogenetic inference • molecular evolution • Markov process • phylogenetic tree • nonhomogenous
Peter Lockhart, Associate Editor