by Charles-Elie Rabier, Vincent Berry, Jean-Christophe Glaszmann, Fabio Pardi, Scornavacca Celine
ISE-M, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
LIRMM, Univ.Montpellier, CNRS, Montpellier, France
IMAG, Univ. Montpellier, CNRS, Montpellier, France
AGAP, CIRAD, Montpellier, France
Our C++ simulator "SimSnappNet" is build on the software "SimSnapp" written by David Bryant and Remco Bouckaert.
D. Bryant, R. Bouckaert, J. Felsenstein, N.A. Rosenberg, A. RoyChoudhury : Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing gene trees in a full coalescent analysis. (Molecular Biology and Evolution, Volume 29, Issue 8, 2012)
SimSnappNet generates SNPs data according to a Markovian process that evolved along gene tree branches. The gene tree is random and is obtained according to the Multispecies Network Coalescent (i.e. a coalescent process that evolves inside a phylogenetic network). Although SNPS data are generated, SimSnappNet returns only count data ....
This count data can be analyzed with SnappNetForSimSnappNet (see the repository on github).
SimSnappNet is described at https://rabier.github.io/doc/SimSnappNet.html