# README file 

# Coral data
103_ddr.bam - 131_ddr.bam	bam files for the ddRADseq coral data
103_epi.bam - 131_epi.bam	bam files for the epiRADseq coral data

coral_pipeline.txt		The analytical pipeline for the coral data
coral_ADO.R				R script to calculate Allelic Dropout for the coral data
coral_Fig1_Fig3.R		R script to make Figure 1 and 3 of the article
Genetic_analysis_corals.R	R script to conduct genetic analysis on the coral data


# whitefish data
ddr_ELT08361.bam - ddr_ELT09287.bam		bam files for the ddRADseq whitefish data
epi_ELT08361.bam - epi_ELT09287.bam		bam files for the epiRADseq whitefish data

ddRAD_epiRAD_pipeline.txt		The analytical pipeline for the whitefish data	
whitefish_ADO.R					R script to calculate Allelic Dropout for the whitefish data
whitefish_Fig1_correlation.R	R script to make Figure 1 and calculate correlation of genetic diversity statistics
genetic_analysis_whitefish.R	R script to conduct genetic analysis on the whitefish data