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MBE Advance Access originally published online on July 20, 2006
Molecular Biology and Evolution 2006 23(10):1976-1983; 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

Research Article

Test a Clade in Phylogenetic Trees

Xiaofei Shi, Hong Gu and Chris Field

Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada

E-mail: shi{at}mathstat.dal.ca.

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 that 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 or the false discovery rate (FDR), 4 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.

Key Words: test • multiple comparison • constraint • clade • FDR


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