I have written a number of scripts for the analysis of RadSeq and whole genome data that can be found on my github site. I am actively using these scripts in my own research, but would be happy to answer any questions or explain them if you might find them useful.

The package rtetracolorspace is an implementation of the analyses presented in Stoddard, M. C. and Prum, R. O. 2008. Evolution of avian plumage color in a tetrahedral color space: a phylogenetic analysis of New World buntings. American Naturalist 171: 755-76. These analyses use the probability of absorption curves for the four retinal cones to plot reflectance spectra within a tetrahedron. These analyses can be conducted for any species that has a tetrachromatic visual system if the user can supply the probability of absorption curves for the four cone types. Currently, a data object with the Blue Tit curves is implemented within the rtetracolorspace package. Functions are provided to calculate the color span, hue disparity, color volume, average chroma, and average brilliance of a distribution of plumage points, as well as the tristimulus color variables for individual points. In addition, functions are provided for the visualization of points within the tetracolorspace.

Currently, scripts for the functions can be downloaded from my github site. Documentation is not yet available, but the scripts are commented to describe each function. An additional implementation, tetracolorspace of these analyses by Stoddard and Prum is written for MatLab.

If you use this package, in addition to citing Stoddard and Prum 2008, please cite: Shultz, A.J., and J.C. Rudy. 2011. Rtetracolorspace: avian tetrahedral color space (R package), url: https://github.com/ajshultz/rtetracolorspace.