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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.

A pretty densitree of the 10 species analysed in this tutorial:

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