By Topic

A Simple and Accurate Method for Rogue Taxon Identification

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

2 Author(s)
Aberer, A.J. ; Exelixis Lab., Heidelberg Inst. for Theor. Studies, Heidelberg, Germany ; Stamatakis, A.

The summary of a phylogenetic analysis (typically a consensus tree) can be substantially biased by so-called rogue taxa (or briefly: rogues). Rogues assume varying phylogenetic positions in the tree collection that is used to build the consensus tree and thereby decrease the resolution of the consensus. We present an accurate and straight-forward algorithm for identifying rogues that assesses the effect on the consensus tree support values by removing one taxon at a time. Our approach improves the resolution of the consensus tree and, at the same time, increases the support values of existing relationships. We compare our algorithm to three competing methods (leaf stability index, taxonomic instability index, and Pattengale's algorithm) on a large number of real biological data sets. We show that it outperforms stability-based methods since rogue taxa are not necessarily the most unstable taxa with respect to stability measures. Our algorithm is more memory-efficient than Pattengale's approach while instances, where Pattengale's algorithm outperforms our approach, appear to be rare on real data. Finally, we find that, it is advisable to conduct a de novo bootstrap analysis after rogues have been removed from the sequence alignment.

Published in:

Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on

Date of Conference:

12-15 Nov. 2011