Journal
BIOINFORMATICS
Volume 22, Issue 10, Pages 1225-1231Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btl064
Keywords
-
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available