TY - JOUR
T1 - Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
AU - Ababneh, Faisal
AU - Jermiin, Lars S.
AU - Ma, Chunsheng
AU - Robinson, John
N1 - Funding Information:
The hospitality of Patrick Forterre and Institut Pasteur is gratefully acknowledged by L.S.J. The authors also wish to thank Keith A Crandall, Simon YW Ho, Vivek Jayaswal and the reviewers for their constructive comments. F.A. was supported by a postgraduate scholarship from the Al-Hussain Bin Talal University in Jordan. This research was partly funded by a Discovery Grant (DP0453173) from the Australian Research Council.
PY - 2006/5/15
Y1 - 2006/5/15
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/btl064
DO - 10.1093/bioinformatics/btl064
M3 - Article
C2 - 16492684
AN - SCOPUS:33646892649
SN - 1367-4803
VL - 22
SP - 1225
EP - 1231
JO - Bioinformatics
JF - Bioinformatics
IS - 10
ER -