Scripts and files for Selection Manuscript

README.txt
	This file

sample_information.csv and its excel equivalent sample_information.xlsx:
	Includes: 	Individual Identifier (ELT)
				sex
				Collection Locations (longitude, latitude, altitude)
				Incubation Days
				Eggshell Thickness
				q-values values from Admixture analysis
				Assigned parity (ovi < 0.05, viv > 0.95 otherwise hyb)
				NCBI sample archive information for WGS (WGS_Run, WGS_Experiment, WGS_SRA)
				NCBI sample archive information for associated RADseq if available (RADSeq_Run, RADSeq_Experiment, RADSeq_SRA)
				Year Sequenced (seq_year)
				WGS coverage information (reads, mapped_reads, median_insert_size, mean_coverage, std_coverage)
				
helper_functions.R
	Functions used throughout analysis

01_Reference_Genome/:
	 - Eastern Oviparous genome files (Eovi.ref.V1.19)
	 - Western Viviparous genome files (GCA_011800845.1)
	 - UG_Zviv_1_match_genbank_to_refseq.txt	
			Links NCBI genseq to refseq linakge group names for GCA_011800845.1 genome


02_VCF_and_Plink_Files/:
	- EO_BCFT_Fully_Filtered_Autosomes.vcf.gz:
		VCF files containing genotypes of autosomes for all individuals
		prior to LD pruning
	- EO_BCFT_Fully_Filtered_Autosomes_0.1.vcf.gz:
		VCF files containing genotypes of autosomes for all individuals
		after LD pruning
	- EO_BCFT_Fully_Filtered_Autosomes_0.1_imputed.vcf.gz:
		VCF files containing genotypes of autosomes for all individuals
		after LD pruning and imputation
	- EO_BCFT_Fully_Filtered_Autosomes_0.1_imputed.vcf.gz.csi
		VCF index file
	- EO_BCFT_Fully_Filtered_Autosomes_0.1_imputed_together.bed
	- EO_BCFT_Fully_Filtered_Autosomes_0.1_imputed_together.bim
	- EO_BCFT_Fully_Filtered_Autosomes_0.1_imputed_together.fam:
		Equivalent plink files
	- org_link_map_pos.bed
	- org_link_map_pos.bim
	- org_link_map_pos.fam
		Plink files of SNPs used for linkage mapping of GCA_011800845.1 genome, bim file includes genomic 
		distances in cM
	- org_link_map_pos.vcf
		VCF files equivalent
	
03_Admixture_Analysis/:
	Bash script for carrying out ADMIXTURE analysis and resulting output files

	
04_Calculating_Fst_and_fixed_SNPs/:
	R script for calculating per-SNP FSTs and identifying lineage specific and monomorphic SNPs
	
05_Basic_pop_stats/:
	R script to calculate basic population statistics using hierfstat
		
06_Entropy_Analysis/:
	- inputdataformat.R
		R script adapted from that provided as part of Entropy (March 2019 -- Vivaswat Shastry) to convert vcf files to correct input format
	- entropy_analysis.sh
		Bash script for carrying out Entropy analysis
	- extracting_relevant_entropy_output.R
		R script for extracting entropy output
	
07_Establish_Transect/:
	- R script to fit a transect line through samples, find point on the line closest to each sample,
	  and calculate distances in km between each of these points on the transect line
	  
08_Transect_Pop_Stats:
	- R script to calculate FIS, linkage disequilibrium, and admixture value modality along the transect 
	
09_Geographic_Clines/:
	- R script for carrying out geographic cline analysis with bgchm

10_Genomic_Clines/:
	- genomic_cline_analysis_aim_loci.R
		R script for carrying out hierarchical model of
		genomic cline with bgchm for ancestrally informative markers and summarising output
	- bgchm_calc_init_values.R
		Script to run 5 hierarchical models with 1000 SNPs each to get starting values for sdc and sdv
	- bgchm_all_loci_sep_runs.sh
	- bgchm_all_loci_sep_runs.R
		Shell script and associated R script to run single loci models in batches of 15,000
	- genomic_cline_analysis_all_loci.R
		Code for combining single loci output and summarising

11_Recombination_Rates/:
	- flo_opts.yaml
		Configuration file for flo
	- chr_matches_between_genome_versions.csv
		Information of relationship between chromosomes in EO genome and WV genome
	- lift_genomic_positions_between_genomes.sh
		Shell script to create chain file between genome version and liftover SNPs used in WV linkage map
		generation to EO genome
	- estimate_recombination_rates.R
		R script to estimate recombination rates along EO genome