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MBE Advance Access published online on July 20, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl065
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted July 18, 2006

Research Articles

Test a Clade in Phylogenetic Trees

Xiaofei Shi 1 *, Hong Gu 1, and Chris Field 1

1 Department of Mathematics and Statistics, Dalhousie University Halifax, N.S. B3H 3J5 Canada

* To whom correspondence should be addressed.
Xiaofei Shi, E-mail: shi{at}mathstat.dal.ca


  Abstract

We develop a new method for testing a portion of a tree (called a clade) based on multiple tests of many 4-taxon trees in this paper. This is particularly useful when the phylogenetic tree constructed by other methods have a clade which is difficult to explain from a biological point of view. The statement about the test of the clade can be made through the multiple P-values from these individual tests. By controlling the familywise error rate (FWER) or the false discovery rate (FDR), four different tree test methods are evaluated through simulation methods. It shows that the combination of the approximately unbiased (AU) test and the FDR controlling procedure provides strong power along with reasonable type I error rate and less heavy computation.

Keywords: Test; Multiple comparison; Constraint; Clade; FDR.
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