R package for testing how many times a trait of interest was regained during evolution (aka independent/separate origin hypotheses).
if you don't have devtools package installed, execute
install.packages("devtools")
To install the indorigin package, run
library(devtools)
install_github("vnminin/indorigin",build_vignettes=TRUE)
Load the package and open the package vignette:
library(indorigin)
vignette("indorigin_methods")
Implementation and illustrations section of the vignette goes through two simulated and one real data example.
M. Sabrina Pankey, Vladimir N. Minin, Greg C. Imholte, Marc A. Suchard, and Todd H. Oakley. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid, PNAS 2014; published ahead of print October 21, 2014, doi:10.1073/pnas.1416574111.