03_R8S

This file contains input files and the results files from running R8S on the ML tree, and on 1000 bootstraps of the ML tree. There are 3 files and 2 folders. 'base_files' is just a holder for some basic R8S input files, that the python script uses
(see below). This folder contains: the r8s executable we used (compiled for macs), the basic r8s.txt input file we used for each r8s analysis (which has data on our fossil calibrations), and a .txt file that contains the ML tree, and 1000 boostrapped trees estimated in RAxML as described in the paper. 'bootstrap_rates.txt' contains the results of the R8S analyses, each family is listed on its own row, and each row has 1001 associated columns. The first column contains the ML rate, subsequent columns contain bootstrap rates (in substitutions/site/myr). This is the main output file produced by the python script (see next). 'run_BS_r8s.py' is a python script that will run r8s on the ML tree and the 1000 bootstrap trees. Before running it, create an empty directory in the same folder as the script called "bootstrap_results", then change the "start_dir" and "tree_file" variables at the top of the script to point to the directory the script is in, and the tree file in the
'base_files' folder respectively. Then run the script using python. Briefly, the script takes each tree from the tree file, makes a r8s input file, runs r8s, then parses the output to extract the rates for each family. It then outputs these to the 'bootstrap_rates.txt' file. Be aware that the script stores all r8s results, which can take a lot of space (about 1GB) when the analyses are all complete.