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CHAPTER 1. INTRODUCTION
2
is built on the evolutionary and population genetics programming framework NEMO
(Guillaume and Rougemont, 2006), with well developed demographic models. The
demographic models of NEMO were kept, although several of these functionalities
were re-coded, respectively adapted to the new functionalities of quantiNEMO.
1.4
License
quantiNEMO is free software: you can redistribute it and/or modify it under the
terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. quantiNEMO is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along
with
quantiNEMO.
If
not,
see
http://www.gnu.org/licenses/.
1.5
Acknowledgments
We are grateful to Yves Rousselle, Patrick Meirmans, Christine Grossen, Claire
Mouton, Olivier Blaser, Ilkka Kronholm, YiJian Huang, and Patrick Flight. These
persons helped us to improve quantiNEMO by reporting bugs and/or great discussions.
1.6
Main features
quantiNEMO consists in several simulation components which may be easily extended. The simulation components with their corresponding parameters are described in more detail in the rest of this manual.
Quantitative traits
quantiNEMO allows the simulation of one to multiple quantitative traits each having
its own specifications. Each trait is defined by one to many loci each with up to 256
alleles. The allelic effects at each locus can be drawn from a normal distribution
or can be set explicitly. Mutations are implemented with several models. The
trait determinism can be purely additive, or include dominance and/or epistatic
interactions among loci. Environmental effects can also be set in different ways.
Neutral markers
quantiNEMO also allows the simulation of neutral markers, such as microsatellites