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Bioinformatics Advance Access originally published online on May 22, 2006
Bioinformatics 2006 22(15):1921-1923; 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

NETGEN: generating phylogenetic networks with diploid hybrids

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

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

*To whom correspondence should be addressed.

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/

Contact: morin{at}cs.unm.edu

Received on April 8, 2006; revised on May 13, 2006; accepted on May 14, 2006

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