Code for Adaptive evolution of MHC class I immune genes and disease associations in coastal juvenile sea turtles
Katherine R. Martin, Kate L. Mansfield, Anna E. Savage

1. MHC_sequence_diversity_statistics.R: generates population genetics statistics on MHC alleles recovered in study

2. allele_count.R: generates histogram of allele count count distribution for C. mydas and C. caretta

3. phylogeny.R: generates figures for Bayesian and maximum likelihood phylogenies

4. supertyping_with_DAPC.R: script for MHC supertype analysis

5. RandomForest_FP_status.R: generates random forest model predicting FP status (FP-positive/FP-negative)

6. RandomForest_TumorTexture.R: generates random forest model predicting FP tumor texture (rough/smooth)

7. RiskRatio_FP_status.R: risk ratio analysis relating alleles to FP status (FP-positive/FP-negative)

8. RiskRatio_FP_status_Bonferroni_corrected.R: risk ratio analysis relating alleles to FP status (FP-positive/FP-negative) with Bonferroni correction

9. RiskRatio_TumorTexture.R: risk ratio analysis relating alleles to tumor texture (rough/smooth)

10. RiskRatio_TumorTexture_Bonferroni_corrected.R: risk ratio analysis relating alleles to tumor texture (rough/smooth) with Bonferroni correction

11. supertype_riskratio_FP_status.R: risk ratio analysis relating MHC alleles to FP status (FP-positive/FP-negative), includes Bonferroni correction in script

12. supertype_riskratio_tumor_texture.R: risk ratio analysis relating MHC alleles to FP tumor texture (rough/smooth)
