Department of Ecology & Evolution

University of Lausanne | Switzerland

Information

• About
  • Citing
  • Download
  • Developer
  • Help
  • Source

Tutorials

• Introduction
  • Windows
  • Mac OS
  • Linux
• Demography
  • Growing pop. I
  • Growing pop. II
  • Colonisation
  • Extinction
• Neutral marker
  • Mutation models
  • Migration
  • Genetic map
• Selection
  • Basic selection
  • selection-mutation-drift equilibrium
  • Mendelian mice
• Coalescence

An individual-based program for the analysis of quantitative traits with explicit genetic architecture in structured populations

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 cite quantiNemo

Samuel Neuenschwander, Frédéric Michaud, Jérôme Goudet; quantiNemo 2: a swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time, Bioinformatics, In press, https://doi.org/10.1093/bioinformatics/bty737

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.zip) 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).

• 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.

• Tutorials

  This is a zip file containing all the tutorials (in a R markdown format) including R script to generate the plots from the tutorial. It also contains all the input files of the quantiNemo simulation.

• Old website & change log of input file

  This is a link to the old version of the site where you can still download quantiNemo 1. Everybody is encouraged to switch to the new version, since there is almost no software regression. We also provide a document which very briefly documents how to adapt your quantiNemo 1 input files into quantiNemo 2 input files.

Main developer

QuantiNemo is a software developed by:

• Frédéric Michaud (current active developer)
• Samuel Neuenschwander (main contributor of QuantiNemo 1 and 2)
• Jérôme Goudet (supervisor of the development)

Getting help

The developper and maintener of QuantiNemo encourage users to take contact with them if they need help of any sort. If you encounter problems while using the software, or if you have any question concerning some specific simulation setup or about the documentation we would appreciate to hear from you. We are always seeking to improve the program, adding key features or solving bugs, and to have a clear documentation so any feedback is welcome.

You can either send us an email using of the address above, or post a bug report in the following github repository: here

Source code and bug report

QuantiNemo is a scientific software. It 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.

Users are welcome and encouraged to report bugs in order to improve quantiNemo. The development of quantiNemo is done on Github, and preferably, bugs should be submitted there. Alternatively, email can be sent to one of the authors.

The source code is available in the github repository