These suit of scripts were developed to perform the following analysis:
- SNPs dataset filtering
- Assessment of population genetic structure
- Selection of environmental data
- Assessment of fine-scale spatial genetic structure
- Identification of outlier (adaptive) loci using pcadapt
- Identification of genotype-environment associations using Redundancy Analyses (RDA) & Mahalanobis distances
- Identification of genotype-environment associations using Latent Factor Mixed Models (LFMM2)
- Plotting detections with a Venn Diagram
- Visual assessment of genotype-environment associations using Redundancy Analyses (RDA) on the candidate loci
- Mapping adaptive genetic variation using Spatial Principal Components (sPCA)
- Predicting adaptive genotypes from RDA models and environmental data