├── .gitignore ├── LICENSE ├── README.md ├── biblatex_macros.tex ├── data ├── README.mdown └── primate-mtDNA.nex ├── figures ├── 2ndpos.png ├── 3rdpos.png ├── README.mdown ├── Tracer_comparison_KDE.png ├── Tracer_comparison_box.png ├── Tracer_comparison_hist.png ├── Tracer_comparison_violin.png ├── beast.png ├── beast_out.png ├── calibration.png ├── ccby.pdf ├── clone.png ├── data.png ├── densitree.png ├── densitree_clades.png ├── figTree_CCD.png ├── figtree.png ├── installCCD0.png ├── link.png ├── logs.png ├── priors.png ├── substitution.png ├── taxa.png ├── tracer_bad.png ├── tracer_better.png ├── tracer_comparison.png ├── tracer_covariance.png ├── tracer_good.png ├── tracer_joint.png ├── tracer_two.png ├── treeannot.png └── treeannot_CCD0.png ├── main.tex ├── master-refs.bib ├── preamble.tex ├── precooked_runs ├── Primates.CCD0_MAP.tree ├── Primates.MCC.tree ├── README.mdown ├── primate-mtDNA.log ├── primate-mtDNA.trees ├── primate-mtDNA_long.log └── primate-mtDNA_long.trees ├── 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