PERMUTREE: PERMUTATIONAL REGRESSION ANALYSIS on TREES Written by Aki Watanabe Contact: awatanabe@bio.fsu.edu (awatanabe@amnh.org) Department of Biological Science Florida State University, Tallahassee, FL SUMMARY This program takes a NEWICK string file and a CSV file of a single continuous variable and conducts a permutational regression analysis on phenotypic and phylogenetic distances to create a histogram of the distribution of regression coefficients. Please note that this program was written in Python version 2.7, thus, the print command is not a proper function. To run the script in later versions, modify “print ” to “print()”. To run: python permutree.py <# of iterations> NB: To run the program, you will need tree.py module to run, which can be downloaded through Peter Beerli's website . You will also need matplotlib and scipy Python packages to run this analysis. OUTPUT 1. Console: regression coefficient and p-value of given data. 2. Console: p-value of observed coefficient relative to distribution. 3. permutree_distn.pdf: histogram of distribution of coefficients in pdf format.