This repository contains the necessary files to run the tutorial on divergence time estimation using genome-scale data.
File description:
data/10s.phys: Alignment of protein-coding genes of 10 primate species in two partitions.
data/10s.tree: Tree of 10 primate species with fossil calibrations.
data/330s.phys: Alignment of 1st and 2nd sites of mitochondrial protein-coding genes of 330 primate species in one partition.
data/330s.tree: Tree of 330 primate species.
doc/phylogenomic-dating.pdf: Book chapter with tutorial.
gH/mcmctree-outBV.ctl: Control file for MCMCTree necessary to set up calculation fo the gradient and Hessian for approximate likelihood calculation.
mcmc/mcmctree.ctl: Control file for MCMCTree to perform MCMC sampling from the posterior distribution of divergence times and rates using the approximate likelihood method.
prior/mcmctree-pr.ctl: Control file for MCMCTree to perform MCMC sampling from the prior distribuiton.
R/analysis.R: Examples of how to summarise the MCMC output and MCMC diagnostics.
src/: Source code of MCMCTree v4.9e.