├── README.md ├── example ├── example.coal ├── example.haps ├── example.sample ├── example.traj ├── exampleAncientHaps.txt ├── exampleAncientSamps.txt ├── example_fig.pdf ├── example_fig.png ├── genetic_map.txt ├── out.epochs.npy ├── out.freqs.npy ├── out.post.npy ├── relate_resample.newick ├── timeBins.txt └── timeBins3.txt ├── hmm_utils.py ├── inference.py ├── plot_traj.py ├── tree_utils.py └── utils ├── z_bins.txt ├── z_logcdf.txt └── z_logsf.txt /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/standard-aaron/clues/HEAD/README.md -------------------------------------------------------------------------------- /example/example.coal: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/standard-aaron/clues/HEAD/example/example.coal -------------------------------------------------------------------------------- /example/example.haps: 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