dmc
Distinguishing among modes of convergent adaptation using population genomic data
This repository contains code associated with Lee and Coop (2017).
1. Scripts to run DMC
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A fully worked example for how to use DMC can be found at dmc_example.md
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Short descriptions of the scripts needed to run DMC found in this repository.
See individual files for more details and example for their usage in context.
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calcNeutralF.R contains code to generate and save F as an R object.
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genSelMatrices_individualModes.R contains functions to generate F^(S)^ for single modes of convergent adaptation.
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genSelMatrices_multipleModes.R contains functions to generate F^(S)^ for multiple modes of convergence.
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calcInvDetSelMatrices_all.R contains scripts to generate all the possible inverses and determinants.
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calcCompositeLike.R contains functions for calculating the composite log-likelihoods for all models.
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getMCLE.R contains functions to get the maximum composite likelihood estimates of parameters for all convergence models.
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2. Scripts associated with the Mimulus and killifish analyses in Lee and Coop (2017)
3. Modified version of mssel, a version of ms [1] that allows for the incorporation of selection at a single site, modified by KL to allow for multiple independent origins of beneficial lineages.
[1] Hudson, R. R. (2002). Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18, 337–338.