{
    "name": "branch_site",
    "title": "The branch-site test for positive selection from Zhang et al. (2005)",
    "result_type": "MultiMixtureModel[Codons[a]]",
    "citation": {
	"type": "article",
	"title": "Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level",
	"year": "2005",
	"author": [ { "name": "Zhang, Jianzhi" }, { "name": "Nielsen, Rasmus" }, { "name": "Yang, Ziheng" } ],
	"journal": { "name": "Molecular biology and evolution", "volume": "22", "number": "12", "pages": "2472--2479"},
	"identifier": [{"type":"doi","id":"10.1093/molbev/msi237"}]
    },
    "call": "SModel.branch_site_test[submodel,fs,omegas,posP,posW,posSelection]",
    "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": "fs",
            "arg_type": "List[Double]",
            "default_value": "~dirichlet[2,1]",
	    "description":"Class frequencies in the background model."
        },
        {
            "arg_name": "omegas",
            "arg_type": "List[Double]",
            "default_value": "~iid[1,uniform[0,1]]",
	    "description":"dN/dS ratios for the first n-1 classes in the background model."
        },
        {
            "arg_name": "posP",
            "arg_type": "Double",
            "default_value": "~beta[1,10]",
	    "description": "The fraction of sites switching to positive selection on the foreground branches."
        },
        {
            "arg_name": "posW",
            "arg_type": "Double",
            "default_value": "~log_gamma[4,0.25]",
	    "description": "The dN/dS ratio for positively selected sites on the foreground branches."
        },
        {
            "arg_name": "posSelection",
            "arg_type": "Int",
            "default_value": "~bernoulli[0.5]",
	    "description": "The model indicator: if 0, the sites only switch to neutrality on the foreground branches.\n If 1 then sites may switch to dN/dS=posW."
        }
    ],
    "extract": "all"
}
