├── .Rhistory ├── .gitignore ├── .pairwise_ld.py.swp ├── BioGenepop.py ├── Demerelate_wrapper.R ├── Examples ├── README.md └── filter_replicates_vcf │ └── example_replicates.txt ├── FDR.R ├── LICENSE ├── Loci_counter.py ├── Loci_filter_from_vcf.py ├── README.md ├── SpaceMix_workflow.R ├── VCF2phy.py ├── VCF_SNP_number_matcher.py ├── VCF_corresponder.py ├── bayenv2_results_miner.py ├── bl_gff_2_annotation.py ├── blast_tab_parser.py ├── compare_maps.py ├── compare_pairs.py ├── correct_geste.py ├── filter_loci_by_vcf.py ├── filter_replicates_vcf.py ├── geste2baypass.py ├── keep_central_snp.py ├── loci2phy.py ├── loci_and_vcf_to_GPhoCS.py ├── loci_consensus.py ├── oldloci2phy.py ├── outlier_removal.py ├── pairLD.R ├── pairwise_ld.py ├── plot_structure.py ├── segregating_loci_finder.py ├── singleton_site_remover.py ├── skyline_creator.py ├── snp_pca.R ├── snp_pca_static.R ├── strcture_filter.py ├── struct_to_distruct.py ├── vcf2bcg.py ├── vcf2dadi.py ├── vcf2dapc.R ├── vcf2fas.py ├── 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