Associated code for manuscript:
Harris M, Kim BY and Garud NR. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. , bioRxiv https://www.biorxiv.org/content/10.1101/2023.06.21.545888v1
The documentation to clean and process the data across all Drosophila species can be found in the DataProcessingAndAnalysis directory. This directory contains the following subdirectories:
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Code_Dmelanogaster: Associated code used to process and analyze data from the both populations of D. melanogaster.
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Code_DsechDsantDteiDmau: Associated code used to process and analyze D. sechellia, D. santomea, D. teissieri and D.mauritiana.
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Code_Dsimulans: Associated code used to process and analyze D. simulans.
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code_misc: Code used for additional analyses.
Code used to run simulations can be found in the Simulations directory. Under this directory there is a directory per simulated scenario with all of its associated code. These include: Bottlenecks, Background selection, Sex Bias, lower X-linked mutation rate, soft and hard sweeps.