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Bioinformatics Advance Access published online on May 22, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl191
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 8, 2006
Revised May 13, 2006
Accepted May 14, 2006

Applications note

NETGEN: generating phylogenetic networks with diploid hybrids

M. M. Morin 1 * and B. M. E. Moret 1

1 Department of Computer Science, University of New Mexico, Albuquerque, New Mexico, USA

* To whom correspondence should be addressed.
M. M. Morin, E-mail: morin{at}cs.unm.edu


  Abstract

Summary: NETGEN is an event-driven simulator that creates phylogenetic networks by extending the birth-death model to include diploid hybridizations. DNA sequences are evolved in conjunction with the topology, enabling hybridization decisions to be based on contemporary evolutionary distances. NETGEN supports variable rate lineages, root sequence specification, outgroup generation, and many other options. This note describes the NETGEN application and proposes an extension of the Newick format to accommodate phylogenetic networks.

Availability: NETGEN is written in C and is available in source form at http://www.phylo.unm.edu/~morin/.

Associate Editor: Keith A Crandall
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