Bayesian molecular clock dating tutorial with genome-scale datasets
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.

Bayesian Molecular Clock Dating Tutorial Using Genome-Scale Data

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.