RT Journal Article
SR Electronic
T1 Computing the Internode Certainty and related measures from partial gene trees
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 022053
DO 10.1101/022053
A1 Kassian Kobert
A1 Leonidas Salichos
A1 Antonis Rokas
A1 Alexandros Stamatakis
YR 2015
UL http://biorxiv.org/content/early/2015/07/06/022053.abstract
AB We present, implement, and evaluate an approach to calculate the internode certainty and tree certainty 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 internode certainty and tree certainty calculations. We implement our methods in RAxML and test them on empirical data sets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any data set should also contain comprehensive trees.