{
    "name": "m1a",
    "synonyms": ["M1a"],
    "result_type": "MixtureModel[Codons[a]]",
    "call": "SModel.m1a[submodel,omega0,p0]",
    "args": [
        {
            "arg_name": "submodel",
            "arg_type": "Function[Double,RevCTMC[a]]",
            "default_value": "function[w,gy94[omega=w]]",
	    "description": "The model as a function of dN/dS"
        },
        {
            "arg_name": "omega0",
            "arg_type": "Double",
            "default_value": "~uniform[0,1]",
	    "description": "The dN/dS value for conserved sites"
        },
        {
            "arg_name": "p0",
            "arg_type": "Double",
            "default_value": "~uniform[0,1]",
	    "description": "The fraction of conserved sites"
        }
    ],
    "description":"A mixture of conserved and neutral sites.  The conserved sites have frequency p0 and dN/dS=omega0.\n\nThe M1a model modifies the M1 model to avoid forcing the conserved dN/dS to 0.",
    "citation":{"type": "article",
		"title": "Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites",
		"year": "2004",
		"author": [{"name": "Wong, Wendy S. W."},
			   {"name": "Yang, Ziheng"},
			   {"name": "Goldman, Nick"},
			   {"name": "Nielsen, Rasmus"}],
		"journal": {"name": "Genetics",
			    "volume": "168",
			    "number": "2",
			    "pages": "1041--1051"},
		"identifier": [{"type":"doi",
				"id":"10.1534/genetics.104.031153 "}]
	       },
    "examples": ["function[w,gy94[omega=w,pi=f1x4]]+m1a","function[w,mg94[omega=w]]+m1a","function[w,fMutSel0[omega=w]]+m1a"],
    "extract": "all",
    "see": ["m2a","m2a_test"]
}
