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PhyloGeoSim 1.0


Developed by Simon Dellicour, Olivier Hardy and Patrick Mardulyn


Description

PhyloGeoSim (for “phylogeographic simulator”) simulates the evolution of DNA sequences 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 generating DNA sequence matrices and genealogies, PhyloGeoSim also allows the computation of several summary statistics, based on both genetic and geographic information, on each simulated data set. 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).


  1. PGSviewer_1.0.beta_161012.jar program

  2. PhyloGeoSim_1.0.beta_manual_060715.pdf manual

  3. PhyloGeoSim_1.0.beta_240414.jar program

  4. PhyloGeoSim_1.0.beta_example_files_161012.zip data files

  5. PhyloGeoSim_1.0.beta_java_classes_240414.zip source code


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.







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UNIVERSITE LIBRE DE BRUXELLEShttp://www.ulb.ac.be/

SOFTWARE

Genetic data analysis or simulation

  1. PhyloGeoSim

Chemical data analysis

Community or ecological data analysis

 
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