Data from: Speciation and introgression between Mimulus nasutus and Mimulus guttatus

Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL

Date Published: July 11, 2014

DOI: http://dx.doi.org/10.5061/dryad.vp645

 

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Title HMM_and_other_major_analyses
Downloaded 49 times
Description This set of scripts recreates most major analyses from our manuscript. This includes PCA analyses, the distribution of nj tress, the distribution of diversity and our hidden Markov Model. This all works with our associated data file.
Download recreateAnalysesANDfigures.R (16.59 Kb)
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Title Processed_data
Downloaded 13 times
Description An R-object containing 'nj.pca.snps' and 'pairwise.focal.mim'. pairwise.focal.mim is a matrix with genotypes for all samples at all SNPS used in nj and PCA analyses. 'pairwise.focal.mim' a list containing 'comps' and 'bounds.' 'comps' - itself a list of all pairwise comparisons between focal samples. For each pairwise comparison between focal samples the number of sites compared & differences between two samples in 1kb windows is contained in a matrix. 'bound' a matrix describing the location of each 1 kb region.
Download brandainEtAlPLoSGen2014.Robj (24.93 Mb)
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When using this data, please cite the original publication:

Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL (2014) Speciation and introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genet 10(6): e1004410. http://dx.doi.org/10.1371/journal.pgen.1004410

Additionally, please cite the Dryad data package:

Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL (2014) Data from: Speciation and introgression between Mimulus nasutus and Mimulus guttatus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vp645
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