Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

Liu S, Hansen MM

Date Published: October 5, 2016

DOI: http://dx.doi.org/10.5061/dryad.0618v

 

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Title empirical data(psmcfa files)
Downloaded 17 times
Description The zip file contains the input files for PSMC from the empirical data of threespine sticklebacks in the study. Seventeen of them are from RAD data, and one of them is from whole genome sequencing data.
Download empirical data(psmcfa files).zip (767.1 Kb)
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Title Generating PSMC input files from simulated data
Downloaded 20 times
Description The file contains a function written in R. This function randomly samples RAD loci from chromosomes simulated by ms (Hudson 2002), and transforms the RAD data into a ".psmcfa" file for PSMC analysis.
Download ms2psmcfa.r (2.221 Kb)
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Title Generating PSMC input files from empirical RAD data
Downloaded 18 times
Description The files contains a script written in R. The script creates input files for PSMC from empirical RAD data using tag files and allele files. Tag files and allele files are generated through pstacks in Stacks v1.13.
Download stacks2psmcfa.r (1.592 Kb)
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Title Plot PSMC results
Downloaded 35 times
Description The file contains functions written in R. The functions are used to visualize the results from PSMC.
Download plotPsmc.r (3.73 Kb)
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When using this data, please cite the original publication:

Liu S, Hansen MM (2017) PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data. Molecular Ecology Resources 17(4): 631-641. http://dx.doi.org/10.1111/1755-0998.12606

Additionally, please cite the Dryad data package:

Liu S, Hansen MM (2016) Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0618v
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