diff --git a/src/nucleic_acid/nucleic_acid.jl b/src/nucleic_acid/nucleic_acid.jl index 7f61b41..48f6b96 100644 --- a/src/nucleic_acid/nucleic_acid.jl +++ b/src/nucleic_acid/nucleic_acid.jl @@ -17,13 +17,11 @@ _πY(mod::NASM) = _πT(mod) + _πC(mod) """ Generate a Q matrix for a `NucleicAcidSubstitutionModel`, of the form: -```math -Q = \begin{bmatrix} -Q_{A, A} & Q_{A, C} & Q_{A, G} & Q_{A, T} \\ -Q_{C, A} & Q_{C, C} & Q_{C, G} & Q_{C, T} \\ -Q_{G, A} & Q_{G, C} & Q_{G, G} & Q_{G, T} \\ -Q_{T, A} & Q_{T, C} & Q_{T, G} & Q_{T, T} \end{bmatrix} -``` +\$Q = \\begin{bmatrix} +Q_{A, A} & Q_{A, C} & Q_{A, G} & Q_{A, T} \\\\ +Q_{C, A} & Q_{C, C} & Q_{C, G} & Q_{C, T} \\\\ +Q_{G, A} & Q_{G, C} & Q_{G, G} & Q_{G, T} \\\\ +Q_{T, A} & Q_{T, C} & Q_{T, G} & Q_{T, T} \\end{bmatrix}\$ """ @inline function Q(mod::NASM) α = _α(mod) @@ -69,13 +67,11 @@ end """ Generate a P matrix for a `NucleicAcidSubstitutionModel`, of the form: -```math -P = \begin{bmatrix} -P_{A, A} & P_{A, C} & P_{A, G} & P_{A, T} \\ -P_{C, A} & P_{C, C} & P_{C, G} & P_{C, T} \\ -P_{G, A} & P_{G, C} & P_{G, G} & P_{G, T} \\ -P_{T, A} & P_{T, C} & P_{T, G} & P_{T, T} \end{bmatrix}. -``` +\$P = \\begin{bmatrix} +P_{A, A} & P_{A, C} & P_{A, G} & P_{A, T} \\\\ +P_{C, A} & P_{C, C} & P_{C, G} & P_{C, T} \\\\ +P_{G, A} & P_{G, C} & P_{G, G} & P_{G, T} \\\\ +P_{T, A} & P_{T, C} & P_{T, G} & P_{T, T} \\end{bmatrix}\$ for specified time """