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quantiNEMO
An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population
quantiNEMO is a software developed by Samuel Neuenschwander, Jérôme Goudet, Frédéric Hospital, and Frédéric Guillaume.
What is quantiNEMO
How to launch quantiNEMO
How to cite quantiNEMO
Available Downloads
Download quantiNEMO
Register as an user
What is quantiNEMO
quantiNEMO is an individual-based, genetically explicit
stochastic simulation program. It was developed to investigate the effects
of selection, mutation, recombination, and drift on quantitative traits
with varying architectures in structured populations connected by
migration and located in a heterogeneous habitat. quantiNEMO is
highly flexible at various levels: population, selection, trait(s)
architecture, genetic map for QTL and/or markers, environment, demography,
mating system, etc.
quantiNEMO is a console program, and is coded in standard C++ using an object oriented approach, runs on any computer platform, and is distributed under an open source license.
How to launch quantiNEMO (Windows version)
To use quantiNEMO, download and
extract the compressed folder quantinemo.zip to a folder of
your choice.
quantiNEMO requires a settings file to launch the simulations. The
user manual describes the possible parameterization. A simulation is
launched by passing the name of the settings file as single parameter to
the executable (e.g. "quantiNEMO.exe settings.txt"). If the settings file
is named quantiNEMO.ini and resides in the same folder as the executable the simulation
can be started without passing the name of the settings file as a
parameter (e.g. "quantiNEMO") in the console, or simply by double clicking
on the executable.
How to
cite quantiNEMO
The program should be cited as follows:
Neuenschwander S, Hospital F, Guillaume F, Goudet J (2008)
quantiNEMO: an individual-based program to simulate quantitative traits with explicit
genetic architecture in a dynamic metapopulation
Bioinformatics 24, 1552-1553. [pdf]
Available downloads
Executable for Windows
This compressed folder (quantinemo_pc.zip) contains all files needed to launch a
simulation on a Windows computer. It consists of the executable for
Windows (quantiNemo.exe), an example settings file (quantiNemo.ini),
and the user manual (quantiNemo.pdf).
Executable for Unix/Linux
This compressed folder (quantinemo_linux.tar.gz) contains all files needed to launch a
simulation on an Unix/Linux computer: It consists of the executable for Unix/Linux
(quantinemo), an example settings file (quantiNemo.ini),
and the user manual (quantiNemo.pdf).
Executable for Macintosh (OS X)
This compressed folder (quantinemo_mac.zip) contains all files needed to launch a
simulation on a Macintosh computer with OS X: It consists of the executable for Mac OS X
(quantiNemo), an example settings file (quantiNemo.ini),
and the user manual (quantiNemo.pdf).
Source code
This compressed folder (quantinemo_src.zip) contains all source code files (*.h
and *.cpp) and a generic makefile (Makefile) for the GNU GCC
compiler. These files allow to generate an executable for any platform
supporting a standard C++ compiler. A sample settings file is also
included (quantiNEMO.ini).
Manual
This is the user manual as a pdf file (quantiNemo.pdf). The user manual describes quantiNEMO
in all its aspects, explains parameters, and shows which
outputs can be generated.
Syntax highlighting
We provide syntax highlighting definitions to improve the readability of the setting files for quantiNEMO. The definition is available for the widely used text editors TextPad (quantinemo.syn) and Notepad++ (Npp_quantiNEMO.zip), however the definition may easily be adapted to any text editor supporting user defined syntax highlighting. The syntax highlighting definition allows a better visibility of the settings file by highlighting parameters, statistics and comments.
last modified on 15.06.2010