Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
Date
2006-05-15Author
Ababneh, Faisal
Jermiin, Lars S.
Ma, Chunsheng
Robinson, John
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Ababneh, F., L. S. Jermiin, et al. (2006). "Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences." Bioinformatics 22(10): 1225-1231.
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 anincreased 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/
Contact: lars.jermiin@usyd.edu.au
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