apal.5x.nc2.mac4.vcf contains vcf file of genotypes for all E. pallida individuals after clone removal, but before filtering for loci with a minimum allele frequency of 5%.
pcadapt_analysis_final.R contains code to perform PCA analysis with pcadapt. This analysis is based on a SNP matrix (SNPmat0.05.txt) of 2577 SNPs that have a minimum allele frequency of 5%. The names of the loci are in locusNames_0.05.txt and information about the population designation for each sample is in pop_file.csv.
Gene set enrichment analyses in ErmineJ used the Gene Annotation file bvpSNPS_erminej.txt and were based on the PC1 loadings in column 3 of PCloadings_final.txt. The file bvpSNPS_erminej.txt contains the AIPGENE models for all SNPs in apal.5x.nc2.mac4.vcf that were present in genic regions (5'UTR, CDS, intron or 3'UTR) as well as GO annotations from the Aiptasia genome v1.0.
out.weir.fst is a file containing Weir and Cockerham FST values output from vcftools for E. pallida from the global lineage vs. the Bocas specific lineage. This was based on the 2577 biallelic SNPs with minimum allele frequency of 5%
