Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Bonnet T, Leblois R, Rousset F, Crochet P

Date Published: June 8, 2017

DOI: http://dx.doi.org/10.5061/dryad.44sv0

 

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Title SourceCode
Downloaded 4 times
Description Source code for the simulation of multi-locus introgression during secondary contacts. After decompression, add the file present at https://github.com/timotheenivalis/CodeAllForward/blob/master/MersenneTwister.h to the directory. The program can then be compiled, for instance, with g++ -o AllForward -O2 *.cpp
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Title AllForward executable
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Description Executable binary of the simulation program.
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Title AllForward option file
Downloaded 5 times
Description Example of an option file to give instructions to AllForward.exe. This file should be placed in the same folder as the program AllForward.exe for the options to be read. This file must be named "AllForward.txt", unless another name is specified in the command line when calling the program.
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Title FunctionsSimul
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Description R Functions used to analyze the simulations. - mtfunc does the general analyzes for one scenario (unique combination of parameters) - WrapMtFunc is a wrapper for a series of scenarios - mtfuncInvasion is a special "mtfunc" for invasion scenarios - mtfuncInvasionAllGrid is similar but uses the full grid in cases of invasion (unlike what we presented in the publication)
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Title ExampleAnalysis
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Description Example of the use of mtfunc() on a series of scenarios. Once the analyses are run for all scenarios, the result files (for instance BDbresults.txt, BDbresultsnofix.txt, and BDbDistriMtMax.txt here) can all be loaded to create AllRData.RData.
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Title AllRData
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Description R data of all the analyzed simulations.
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Title Graphes
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Description Knitr (R+Latex) code used to produce the graphes in the publication. (needs AllRData.RData)
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Title README
Downloaded 6 times
Description This package contains the code used to simulate and analyze the data used in the publication.
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When using this data, please cite the original publication:

Bonnet T, Leblois R, Rousset F, Crochet P (2017) A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Evolution, online in advance of print. http://dx.doi.org/10.1111/evo.13296

Additionally, please cite the Dryad data package:

Bonnet T, Leblois R, Rousset F, Crochet P (2017) Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.44sv0
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