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Bioinformatics Advance Access published online on December 1, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl614
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 21, 2006
Revised November 25, 2006
Accepted November 28, 2006

Applications note

The automation of Nested Clade Phylogeographic Analysis

Mahesh Panchal 1 *

1 School of Biological Sciences, University of Reading, Whiteknights, P.O. Box 228, Reading RG6 6AJ, UK

* To whom correspondence should be addressed.
Mahesh Panchal, E-mail: m.panchal{at}rdg.ac.uk


  Abstract

Summary: ANeCA is a fully automated implementation of Nested Clade Phylogeographic Analysis (NCPA). This was originally developed by Templeton and colleagues, and has been used to infer, from the pattern of gene sequence polymorphisms in a geographically structured population, the historical demographic processes that have shaped its evolution. Until now it has been necessary to perform large parts of the procedure manually. We provide a program that will take data in Nexus sequential format, and directly output a set of inferences. The software also includes TCS v1.18 and GeoDis v2.2 as part of automation.

Availability: The software is available free of charge from http://www.rubic.rdg.ac.uk/~mahesh/software.html. The program is written in Java and requires the Java 1.4 Runtime Environment (or later) to run. The source code is included in the package, and includes the source from TCS and GeoDis. ANeCA, TCS, and GeoDis, are released under the GNU General Public License.

Associate Editor: Keith A Crandall
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