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Computational Molecular Evolution$
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Ziheng Yang

Print publication date: 2006

Print ISBN-13: 9780198567028

Published to Oxford Scholarship Online: April 2010

DOI: 10.1093/acprof:oso/9780198567028.001.0001

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Comparison of methods and tests on trees

Comparison of methods and tests on trees

(p.185) 6 Comparison of methods and tests on trees
Computational Molecular Evolution


Oxford University Press

This chapter discusses two problems: the evaluation of statistical properties of tree reconstruction methods and tests of the significance of estimated phylogenies. Section 6.1 discusses criteria for assessing the statistical properties of tree reconstruction methods. A summary of simulation studies conducted to evaluate different methods is provided, as well as some recommendations concerning the use of those methods in practical data analysis. Sections 6.2 and 6.3 deal with the likelihood versus parsimony debate from the likelihood and parsimony perspectives, respectively. Section 6.4 provides an overview of methods for assessing the reliability of estimated phylogenies.

Keywords:   phylogentic tree, tree reconstruction, likelihood estimation, parsimony methods

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