Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a measure of the evolutionary change between any pair of the extant taxa. A standard technique is to use the log det formula to construct pairwise distances from aligned sequence data. We review a distance measure valid for the most general models, and show how the log det formula can be used as an estimator thereof. We then show that the foundation upon which the log det formula is constructed can be generalized to produce a previously unknown estimator which improves the consistency of the distance matrices constructed from the log det formula. This distance estimator provides a consistent technique for constructing quartets from phylogenetic sequence data under the assumption of the most general Markov model of sequence evolution. © 2006 Elsevier Inc. All rights reserved.

Item Type:	Refereed Article
Research Division:	Physical Sciences
Research Group:	Other physical sciences
Research Field:	Other physical sciences not elsewhere classified
Objective Division:	Expanding Knowledge
Objective Group:	Expanding knowledge
Objective Field:	Expanding knowledge in the physical sciences
UTAS Author:	Sumner, JG (Dr Jeremy Sumner)
UTAS Author:	Jarvis, PD (Dr Peter Jarvis)
ID Code:	41367
Year Published:	2006
Funding Support:	Australian Research Council (DP0344996)
Web of Science® Times Cited:	11
Deposited By:	Physics
Deposited On:	2006-08-01
Last Modified:	2007-03-21
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