PhyloGeoSim 2.0
Developed by Simon Dellicour, Olivier Hardy and Patrick Mardulyn
Description
PHYLOGEOSIM 2.0 (for “phylogeographic simulator”) simulates the evolution of DNA sequences, microsatellites or SNPs under a model of coalescence on a 2-dimensional grid in which each cell is treated as one population. Going backward in time, populations can exchange gene copies and/or host coalescence events between two or more gene copies, at each generation. This geographic model of coalescence can be used to simulate data sets under evolutionary scenarios taking both demographic and geographic characteristics into account (e.g. isolation by distance, fragmentation, expansion, secondary contact, …). In addition to generate datasets of genetic variation and gene genealogies, PHYLOGEOSIM also allows, in the case of DNA sequence data, the computation of several summary statistics, based on both genetic and geographic information. Users can use this set of statistics to compare different evolutionary scenarios or to estimate population genetic parameters. PHYLOGEOSIM is an open source software written in Java and can thus be run on any operating system on which a Java Virtual Machine is installed (e.g. Windows, Mac OS and Linux).
See also PGSviewer 2.0, a JavaScript application that allows visualising the evolution of effective population size matrices during forward simulations performed in the same way as PHYLOGEOSIM. PGSviewer uses the same input files and stops at the end of the forward simulation. This can be useful before launching a big set of simulations with PHYLOGEOSIM in order to check if the forward simulation corresponds to the evolutionary scenario implemented by the user. PGSviewer 2.0 is a JavaScript application compiled from a R script with the “shiny” package. To use PGSviewer 2.0 and generate an animated GIF display the forward simulation, follow the different steps described in the manual.
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PhyloGeoSim_2.0.beta_210319.jar program
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PhyloGeoSim_2.0.beta_example_files.zip data files
How to cite PhyloGeoSim
Dellicour S, Kastally C, Hardy OJ, Mardulyn P (2014) Comparing phylogeographic hypotheses by simulating DNA sequences under a spatially explicit model of coalescence. Molecular Biology and Evolution 31, 3359-3372.
