Solanum_habrochaites_popgen

Scripts and files used for popgen analyses of Solanum habrochaites. Included are files for Isolation by Distance with three data sets include all, Northern, and Southern ranges; Principal Compnenent Analyses using SNPRelate; R plotting scripts including strip plots of heterozygosity and plotting the coalescent tree onto a map using phytools; SNAPP analyses; scripts for SNP calling and filtering used to generate downstream files; Structure analyses using the R package LEA; and TreeMix analyses.