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Mol Biol Evol. 2016 Jun;33(6):1606-17. doi: 10.1093/molbev/msw040. Epub 2016 Feb 25.

Computing the Internode Certainty and Related Measures from Partial Gene Trees.

Author information

1
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Kassian.Kobert@gmail.com.
2
Department of Molecular Biophysics and Biochemistry, Yale University Department of Biological Sciences, Vanderbilt University.
3
Department of Biological Sciences, Vanderbilt University Department of Biomedical Informatics, Vanderbilt University Medical Center.
4
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Postfach 6980, Karlsruhe, 76128, Germany.

Abstract

We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set.

KEYWORDS:

bipartition frequencies; clade support; gene trees; internode certainty.

PMID:
26915959
PMCID:
PMC4868120
DOI:
10.1093/molbev/msw040
[Indexed for MEDLINE]
Free PMC Article

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