This directory contains scripts used for estimating rates of evolution across the genome
for clades and for body size.

To compare rates of substitution between clades, we used LINTRE. Code is provided in lintre.sh.

To compare rates of substitution between giant vertebrates and other vertebrates, we used PAML.
The PAML input tree annotated for giant branches is provided, as are the control files for
fitting the null vs. alternative models of a strict clock vs. branches leading to giant taxa
differing in rate.

Also provided is the treePL input file for taking a tree in units of branches of substitutions
and estimating divergence times based on fossil calibrations, which is used for CAFE analyses.