Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Computing the Internode Certainty and related measures from partial gene trees

Kassian Kobert, Leonidas Salichos, Antonis Rokas, Alexandros Stamatakis
doi: https://doi.org/10.1101/022053
Kassian Kobert
1Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Leonidas Salichos
2Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Antonis Rokas
3Vanderbilt University, Department of Biological Sciences, 37235 Nashville, USA
4Vanderbilt University Medical Center, Department of Biomedical Informatics, 37232 Nashville, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alexandros Stamatakis
1Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
5Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted July 06, 2015.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Computing the Internode Certainty and related measures from partial gene trees
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Computing the Internode Certainty and related measures from partial gene trees
Kassian Kobert, Leonidas Salichos, Antonis Rokas, Alexandros Stamatakis
bioRxiv 022053; doi: https://doi.org/10.1101/022053
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Computing the Internode Certainty and related measures from partial gene trees
Kassian Kobert, Leonidas Salichos, Antonis Rokas, Alexandros Stamatakis
bioRxiv 022053; doi: https://doi.org/10.1101/022053

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4113)
  • Biochemistry (8815)
  • Bioengineering (6518)
  • Bioinformatics (23459)
  • Biophysics (11789)
  • Cancer Biology (9207)
  • Cell Biology (13322)
  • Clinical Trials (138)
  • Developmental Biology (7436)
  • Ecology (11409)
  • Epidemiology (2066)
  • Evolutionary Biology (15149)
  • Genetics (10436)
  • Genomics (14043)
  • Immunology (9171)
  • Microbiology (22153)
  • Molecular Biology (8812)
  • Neuroscience (47566)
  • Paleontology (350)
  • Pathology (1428)
  • Pharmacology and Toxicology (2491)
  • Physiology (3730)
  • Plant Biology (8079)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2220)
  • Systems Biology (6037)
  • Zoology (1253)