manuscript_DRYADscripts

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.

1. pca, treemix, map

2. baypass

3. parallelism randomizations

4. experiment to nature randomizations

5. sex chromosome randomizations

6. structural and functional annotations perl script

Here are the scripts in the folder and description of the scripts

• 1. runBaypassFork.pl = perl fork script to learn multiple mcmc chains for baypass

  2. sexchromrandom.R = randomization tests for presence of host-associated SNPs on Z

  3. effSigns_top58snps.R = randomization tests for effect signs of parallelism SNPs

  4. effSigns_quantiles_randomization.R

  5. effSigns_quantiles_prerandomization.R