This is a README file for several scripts that were used in this paper. All were written by Ben Evans and please contact Ben if you have questions or would like to access the intermediate files that were used as input for these scripts in order to replicate results reported in the paper. All of these intermediate files can be generated from the vcf files that are also in this repository.

These scripts were used for permutation tests for fst (All_N_mt_allinteract_fst_permutation.pl), pi (All_N_mt_allinteract_pi_permutation.pl), dN/dS (All_N_mt_allinteract_paml_permutation.pl), Tajima's D and Fay and Wu's H (All_N_mt_allinteract_stat_column_permutation.pl) and runs of homozygosity (ROH_permutation.pl):
* All_N_mt_allinteract_fst_permutation.pl
* All_N_mt_allinteract_paml_permutation.pl
* All_N_mt_allinteract_pi_permutation.pl
* All_N_mt_allinteract_stat_column_permutation.pl
* ROH_permutation.pl

These are input files for some of the permutation scripts that were generated by parsing the gff file for the MacaM reference genome:
* all_mRNA.gff
* FINAL_OXPHOS_ARP2_MRP_MTREPLICATION_allinteractexceptC2_andallother_genez_orientation.txt

This is a script that performs a block jacknife in order to obtain confidence intervals for Fst, Patterson's D, and fDM:
* Does_block_jackknife.pl

These are permutation scripts that were used to asssess the probability of the observed number of Ninterct genes on introgression blocks in two admixed individuals:
* Introgression_block_permutation_PF511_homoz_introgression.pl
* Introgression_block_permutation_PF626_homoz_introgression.pl

These are scripts that were used to fit linear models and perform outlier analyses on Tajima's D (N_interact_TajD.R), Fay and Wu's H (N_interact_FWH.R), pi (N_interact_pi.R), fst (), and runs of homozygosity (ROH.R). 
* N_interact_FWH.R
* N_interact_TajD.R
* N_interact_pi.R
* ROH.R

There are also vcf files for each chromosome in the study, which are filtered as detailed in the paper.  Please note that the PAR of the chrX has been removed.  The naming of the 20 chromosomes follows the MacaM genome (including chr2a and chr2b).
