QUETZAL
The Coalescence Template Library
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Introduction

QuetzalCoaTL (Coalescence Template Library), or Quetzal for shorter use, is a C++ template library for simulating coalescence processes in spatially explicit landscapes with complex demography.

If you are a scientist interested in studying how populations grow and spread in complex environments using Approximate Bayesian Computation (ABC), this library can offer you some useful tools for building programs based on complex generative models of genetic data.

Check the founder article introducing the library.

  • Because of ABC is computationally intensive, we wanted Quetzal to be fast enough to run millions of simulations in a minimal amount of time.
  • Because the set of all possible simulation models is infinite, we wanted Quetzal to be modular, so you could feel free to recombine the tools we offer in the way which is most desirable for your own purpose.
  • Because you will surely come with your own project bringing many specificities which would be impossible for us to foresee, we wanted Quetzal to be extensible, so you can develop your own tools and combine them with minimal cost with Quetzal interfaces.

And because this project is still in development, it is naturally modest and still focused on our specific needs. This is why Quetzal lacks of what could seem to you as basics : please feel free to contact us for feedbacks or collaboration !

Overview

Most of the Quetzal modules (geography, expressive, demography, random, coalescence) will help you to implement an open-ended number of coalescence-based models variants.

The abc module helps you to efficiently embed the simulation code in an ABC framework to estimate the model parameters.

modules.png
Environmental demo-genetic model framework and Quetzal modules

About

Maintainer: Arnaud Becheler

How to cite: see the founder article

Community: IRC channel #quetzal on Freenode

Supported platform: Linux

Contribute: Check our Github repository and use the Pull Request system

Clone:

git clone https://github.com/Becheler/quetzal.git

Acknowledgment

The founding version of Quetzal was basically the implementation of the probabilistic model of biological invasion developed during the PhD thesis of Arnaud Becheler under the direction of Stephane Dupas (laboratoire d'Evolution, Génomes, Comportements et Ecologie de Gif-sur-Yvette) and Camille Coron (Laboratoire de Mathématiques d'Orsay).

Quetzal benefits from the constant support and feedbacks of Florence Jornod, who initially contributed to Quetzal as an intern.

The PhD project was funded by the BASC labex.