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MBE Advance Access published online on October 19, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl153
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 17, 2006

Research Article

Performance of a New Invariants Method on Homogeneous and Non-homogeneous Quartet Trees

M. Casanellas 1 * and J. Fernáandez-Sáanchez 1

1 Dpt. Matemàtica Aplicada I Universitat Politècnica de Catalunya, Barcelona, Spain

* To whom correspondence should be addressed.
M. Casanellas, E-mail: marta.casanellas{at}upc.edu


  Abstract

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 authors (the initial idea due to Lake (Lake, 1987) and Cavender and Felsenstein (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 non-homogeneous models on phylogenetic trees.


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