Population structure in Quercus suber L. revealed by nuclear microsatellite markers - paper scripts
Script used to make the paper's PCA analyses. The data filenames are hard-coded in the file, but everything is quite self-explanatory. In order to run the script, just modify the path to the input files to match that of your filesystem and it's ready to use.
Script used to create Fst dendrograms. Ended up not being used in the paper, but since it had been written we decided it was a good a idea to leave it here, both as a reference, and in case it might be of use to someone else.
Script used to calculate the t-test for the FIS values. It's so simple it didn't warrant any special documentation.
Python script based on the one from pyRona used to draw the plot from figure 1. Requires cartopy, numpy and matplotlib.
Takes 3 arguments: sample_coords.csv, output.svg and shapefile.shp
It will draw a map, based on the sample coordinates, with the distribution shapefile superimposed.
Genepop formatted file containing microssatellite alleles (17 populations and 13 loci)
Genepop formatted file containing 'neutral' microssatellite alleles (17 populations and 11 loci)
Tab-separated pairwise Fst triangular matrix required for Fst_dendro.R. Like the script that requires it, this file ended up not being used in the paper itself.
Tab-separated file containing FIS values per microssat, each column has values calculated from different population arrangements
Tab-separated file containing sampling site coordinates. First column is sample name, second is Latitude, third is Longitude.
Not yet available.