A comparison of methods for estimating the transition:transversion ratio from DNA sequences

Molecular Phylogenetics and Evolution
A K Kristina Strandberg, Laura A Salter

Abstract

Estimation of the ratio of the rates of transitions to transversions (TI:TV ratio) for a collection of aligned nucleotide sequences is important because it provides insight into the process of molecular evolution and because such estimates may be used to further model the evolutionary process for the sequences under consideration. In this paper, we compare several methods for estimating the TI:TV ratio, including the pairwise method [TREE 11 (1996) 158], a modification of the pairwise method due to Ina [J. Mol. Evol. 46 (1998) 521], a method based on parsimony (TREE 11 (1996) 158), a method due to Purvis and Bromham [J. Mol. Evol. 44 (1997) 112] that uses phylogenetically independent pairs of sequences, the maximum likelihood method, and a Bayesian method [Bioinformatics 17 (2001) 754]. We examine the performance of each estimator under several conditions using both simulated and real data.

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Citations

Aug 26, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hari RamVed Pal Singh
Sep 1, 2012·Molecular Biology and Evolution·Kevin VannesteSteven Maere
Nov 28, 2012·Plant Molecular Biology·Pedro J Martínez-GarcíaCarlos H Crisosto
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Irina AbnizovaTony Cox
Jan 25, 2006·Journal of Theoretical Biology·Hervé SeligmannBasuthkar J Rao

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