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Bioinformatics Advance Access published online on July 31, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl415
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 5, 2006
Revised July 24, 2006
Accepted July 26, 2006

Applications note

Nemo: an evolutionary and population genetics programming framework

Frédéric Guillaume 1 * and Jacques Rougemont 2

1 Department of Ecology and Evolution, University of Lausanne, Biofore, CH-1015 Lausanne, Switzerland; Department of Zoology, University of British Columbia, 6270 University blvd, Vancouver, British Columbia, V6T 1Z4, Canada
2 Vital-IT, Swiss Institute of Bioinformatics, Quartier Sorge-Genopode, CH-1015 Lausanne, Switzerland

* To whom correspondence should be addressed.
Frédéric Guillaume, E-mail: guillaum{at}zoology.ubc.ca


  Abstract

Summary: Nemo is an individual-based, genetically explicit, and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutralmarkers, and more), life cycle events (mating, dispersal, aging, selection, etc.), and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments.

Availability: The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.

Associate Editor: Martin Bishop
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