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Bioinformatics Advance Access published online on February 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl064
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 23, 2005
Revised February 15, 2006
Accepted February 19, 2006

Article

Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences

Faisal Ababneh 1, Lars S. Jermiin 2 *, Chunsheng Ma 3, and John Robinson 1

1 School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
2 School of Biological Sciences, University of Sydney, NSW 2006, Australia; Sydney University Biological Informatics and Technology Centre, University of Sydney, NSW 2006, Australia; Unité de Biologie Moléculaire de Gène chez les Extrêmophiles, Institut Pasteur, 75724 Paris Cedex, France
3 Department of Mathematics and Statistics, Wichita State University, Wichita, Kansas 67260-0033, USA

* To whom correspondence should be addressed.
Lars S. Jermiin, E-mail: lars.jermiin{at}usyd.edu.au


  Abstract

Motivation: Most phylogenetic methods assume that the sequences of nucleotides or amino acids have evolved under stationary, reversible, and homogeneous conditions. When these assumptions are violated by the data, there is an increased probability of errors in the phylogenetic estimates. Methods to examine aligned sequences for these violations are available, but they are rarely used, possibly because they are not widely known or because they are poorly understood.

Results: We describe and compare the available tests for symmetry of k-dimensional contingency tables from homologous sequences, and develop two new tests to evaluate different aspects of the evolutionary processes. For any pair of sequences, we consider a partition of the test for symmetry into a test for marginal symmetry and a test for internal symmetry. The proposed tests can be used to identify appropriate models for estimation of evolutionary relationships under a Markovian model. Simulations under more or less complex evolutionary conditions were done to display the performance of the tests. Finally, the tests were applied to an alignment of small-subunit ribosomal RNA sequences of five species of bacteria to outline the evolutionary processes under which they evolved.

Availability: Programs written in R to do the tests on nucleotides are available from http://www.maths.usyd.edu.au/u/johnr/testsym/.

Associate Editor: Keith A Crandall
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