This the list of all the scripts I could possibly deposit to DRYAD for the host plant manuscript. I have created a folder on the cluster with the following path:
/uufs/chpc.utah.edu/common/home/u6007910/projects/lmelissa_hostAdaptation/manuscriptScripts
This has all the final scripts for the analysis and each code has a description.
pca, treemix, map
baypass
parallelism randomizations
experiment to nature randomizations
sex chromosome randomizations
structural and functional annotations perl script
Here are the scripts in the folder and description of the scripts
runBaypassFork.pl = perl fork script to learn multiple mcmc chains for baypass
sexchromrandom.R = randomization tests for presence of host-associated SNPs on Z
effSigns_top58snps.R = randomization tests for effect signs of parallelism SNPs
effSigns_quantiles_randomization.R
effSigns_quantiles_prerandomization.R