Files and Instructions associated with this paper:
Uy, J.A.C., E.A. Cooper, S. Cutie, M.R. Concannon, J.W. Poelstra, R.G. Moyle, and C.E. Filardi. 2016. Mutations in different pigmentation genes are associated with parallel melanism in flycatchers. Proc. of the Royal Soc. B. 283 20160731.
Contains documents describing all molecular lab protocols for creating the ddRAD-seq Illumina library.
All scripts as well as detailed instructions for running the bioinformatics pipeline to generate SNP calls from de novo assembled ddRAD tags.
Detailed instructions, as well as helpful R scripts, for running GWAS using either the GEMMA software package or the GAPIT R package. For the paper associated with this repository, follow the instructions for running the GEMMA LMM with an externally run PCA (in Plink).