{
    "name": "gy94_ext",
    "result_type": "RevCTMC[Codons[a]]",
    "constraints": ["Nucleotides[a]"],
    "title": "An extended version of the Goldman & Yang (1994) model of dN\/dS",
    "call": "SModel.Codons.gy94_ext[nuc_model,omega,SModel.Frequency.frequencies_from_dict[a,pi],a]",
    "args": [
        {
            "arg_name": "nuc_model",
            "arg_type": "ExchangeModel[a]",
            "alphabet": "getNucleotides[@a]",
            "description": "Symmetric exchange rates on nucleotides"
        },
        {
            "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[@a],1]",
	    "description": "Letter frequencies"
        },
        {
            "arg_name": "a",
            "arg_type": "a",
	    "default_value": "getAlphabet",
	    "description": "The codon alphabet"
        }
    ],
    "description": "This is a version of the gy94 model that has been extended to use user-supplied exchangabilty matrix `nuc_model` on nucleotides.  The original gy94 model distinguishes only between transitions and transversions, and is equivalent to `gy94_ext[hky85_sym]`.",
    "examples": ["gy94_ext[hky85_sym[kappa=2],omega=2]","gy94_ext[gtr_sym,pi=f1x4]"],
    "citation": {"type": "article",
		 "title": "A codon-based model of nucleotide substitution for protein-coding DNA sequences",
		 "author": [{"name": "Goldman, Nick"},{"name": "Yang, Ziheng"}],
		 "journal": {"name": "Molecular biology and evolution",
			     "volume":"11",
			     "number":"5",
			     "pages":"725--736"},
		 "year":"1994",
		 "link":[{"url":"http://www.genetics.org/content/148/3/929.short"}]
		},
    "see": ["gy94"],
    "extract": "all"
}
