files related to squamate parity project bisse.rmd will estimate best-fit BiSSE models on a collection of time-scaled trees. Simply place it in the directory with the files you'd like to estimate models for and run it. Makefile reproduces full analyses. + Dependencies: plot.py, plot_support.py, bisse.rmd, splitbisse.r and a directory one directory up called 'trees' full of trees with the ending '.tre'