{
    "name": "mg94k",
    "deprecated-synonyms": ["MG94"],
    "result_type": "RevCTMC[Codons[a]]",
    "constraints": ["Nucleotides[a]"],
    "call": "SModel.Codons.mg94k[a,kappa,SModel.Frequency.frequencies_from_dict[Alphabet.getNucleotides[a],pi],omega]",
    "args": [
        {
            "arg_name": "kappa",
            "arg_type": "Double",
            "default_value": "~log_normal[log[2],0.25]",
            "description": "Transition\/transversion ratio"
        },
        {
            "arg_name": "omega",
            "arg_type": "Double",
            "default_value": "~uniform[0,1]",
            "description": "Relative rate of non-synonymous changes relative to synonymous changes"
        },
        {
            "arg_name": "pi",
            "arg_type": "List[Pair[String,Double]]",
            "default_value": "~dirichlet_on[letters[getNucleotides[@a]],1.0]",
	    "description": "Nucleotide frequencies"
        },
        {
            "arg_name": "a",
            "arg_type": "a",
            "default_value": "getAlphabet",
	    "description": "The alphabet"
        }
    ],
    "title": "The Muse & Gaut (1994) model of codon substitution.",
    "citation": {
	"type": "article",
	"title": "A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.",
	"year": "1994",
	"author": [{"name": "Muse, Spencer V"}, {"name": "Gaut, Brandon S"}],
	"journal": {"name": "Molecular biology and evolution", "volume": "11", "number": "5", "pages": "715--724"},
	"link": [{"url":"https://academic.oup.com/mbe/article/11/5/715/1008710"}]
    },
    "description": "The MG94K model extends the MG94 model to account for different rates of transitions and transversions.\n\nThe MG94K model is equivalent to the following models:\n\n  hky85+x3+dNdS\n\n  mg94_ext[hky85]",
    "see": ["mg94","mg94_ext"],
    "extract": "all"
}
