PT  - JOURNAL ARTICLE
AU  - Kassian Kobert
AU  - Leonidas Salichos
AU  - Antonis Rokas
AU  - Alexandros Stamatakis
TI  - Computing the Internode Certainty and related measures from partial gene trees
AID  - 10.1101/022053
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 022053
4099  - http://biorxiv.org/content/early/2016/02/10/022053.short
4100  - http://biorxiv.org/content/early/2016/02/10/022053.full
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 include trees containing the full species set.