{
    "name": "mg94_ext",
    "result_type": "RevCTMC[Codons[a]]",
    "constraints": ["Nucleotides[a]"],
    "call": "SModel.Codons.mg94_ext[a,omega,nuc_model]",
    "args": [
        {
            "arg_name": "nuc_model",
            "arg_type": "RevCTMC[a]",
            "alphabet": "getNucleotides[@a]",
            "description": "Nucleotide substitution rate matrix"
        },
        {
            "arg_name": "omega",
            "arg_type": "Double",
            "default_value": "~uniform[0,1]",
            "description": "Relative rate of non-synonymous changes relative to synonymous changes"
        },
        {
            "arg_name": "a",
            "arg_type": "a",
            "default_value": "getAlphabet",
	    "description": "The alphabet"
        }
    ],
    "title": "An extended version of 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": "This is a version of the mg94 model that has been extended to use a user-supplied rate matrix `nuc_model` on nucleotides.  The original mg94 model is equivalent to `mg94_ext[f81]`.",
    "examples": ["mg94_ext[hky85[kappa=2],omega=2]","mg94_ext[gtr]"],
    "see": ["mg94"],
    "extract": "all"
}
