Fig 1.
The graphical representation of the probabilistic model defined in Example 1.
Fig 2.
A screenshot of LPhy Studio showing the probabilistic graphical model on the left panel (constants hidden), and the auto-generated text description of the data and phylogenetic model on the right panel.
Fig 3.
A screenshot of LPhyStudio showing the GT16 substitution and GT16 error model [27, 44].
The left panel shows the graphical model representation, the right panel shows the simulated tree and diploid nucleotide genotypes, and the bottom panel shows the LPhy script.
Fig 4.
Model validation for the GT16 substitution model and GT16 error model.
Each plot shows the 95% highest posterior density for model parameters: allelic dropout error δ, sequencing/amplification error ϵ, equilibrium frequency for πAA, relative rate rAC, tree height, and tree length.