{
    "name": "RNA.m16a",
    "synonyms": ["shh01_m16a","RNA.shh01_m16a"],
    "constraints": [ "Doublets[a,b]" ],
    "result_type": "RevCTMC[a]",
    "title": "Exchangability matrix on doublets constructed from nucleotide exchange rates",
    "call": "SModel.Doublets.rna_stem_16a[a,aS,aD,b,g,e,SModel.Frequency.frequencies_from_dict[a,pi]]",
    "citation":{"type": "article",
		"title": "RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods",
		"year": "2001",
		"author": [{"name": "Savill, Nicholas J."}, {"name": "Hoyle, David C."}, {"name": "Higgs, Paul G."}],
		"journal": {"name": "Genetics Society of America", "volume": "157", "pages": "399--411"},
		"identifier": [{"type":"pmid","id":"11139520"}]
	       },
    "args": [
        {
            "arg_name": "aS",
            "arg_type": "Double",
            "default_value": "~log_normal[log[2],0.25]",
	    "description": "Exchange rate: 1 change, match <-> match"
        },
        {
            "arg_name": "aD",
            "arg_type": "Double",
            "default_value": "~log_normal[log[2],0.25]",
	    "description": "Exchange rate: 2 changes, match <-> match, both transitions"
        },
        {
            "arg_name": "b",
            "arg_type": "Double",
            "default_value": "~log_normal[log[2],0.25]",
	    "description": "Exchange rate: 2 changes, match <-> match, both transversions"
        },
        {
            "arg_name": "g",
            "arg_type": "Double",
            "default_value": "~log_normal[log[2],0.25]",
	    "description": "Exchange rate: 1 changes, match <-> mismatch"
        },
        {
            "arg_name": "e",
            "arg_type": "Double",
            "default_value": "~log_normal[log[2],0.25]",
	    "description": "Exchange rate: 1 changes, mismatch <-> mismatch"
        },
        {
            "arg_name": "pi",
            "arg_type": "List[Pair[String,Double]]",
            "default_value": "~dirichlet_on[letters[@a],1]",
	    "description": "Doublet frequencies"
        },
        {
            "arg_name": "a",
            "arg_type": "a",
            "default_value": "getAlphabet",
	    "description": "The Doublets alphabet"
        }
    ],
    "description": "Exchangability matrix for rna stems that allows 2 simultaneous changes.\n\nNote the exchange rate for double changes involving a mismatch is 0.",
    "examples": ["RNA.m16a","RNA.m16a+Rates.free"],
    "see": ["x2_sym"]
}
