LanGen_pipeline

These suit of scripts were developed to perform the following analysis:

1. SNPs dataset filtering
2. Assessment of population genetic structure
3. Selection of environmental data
4. Assessment of fine-scale spatial genetic structure
5. Identification of outlier (adaptive) loci using pcadapt
6. Identification of genotype-environment associations using Redundancy Analyses (RDA) & Mahalanobis distances
7. Identification of genotype-environment associations using Latent Factor Mixed Models (LFMM2)
8. Plotting detections with a Venn Diagram
9. Visual assessment of genotype-environment associations using Redundancy Analyses (RDA) on the candidate loci
10. Mapping adaptive genetic variation using Spatial Principal Components (sPCA)
11. Predicting adaptive genotypes from RDA models and environmental data