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    },
   "alphabet":    {
{"AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA", "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT", "CAA", "CAC", "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG", "CGT", "CTA", "CTC", "CTG", "CTT", "GAA", "GAC", "GAG", "GAT", "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA", "GTC", "GTG", "GTT", "TAC", "TAT", "TCA", "TCC", "TCG", "TCT", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG", "TTT"} 
    },
   "bases":    {
{"A", "C", "G", "T"} 
    },
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   "constrain-branch-length":"models.codon.MG_REV.ConstrainBranchLength",
   "defineQ":"models.codon.MG_REV._DefineQ",
   "description":"The Muse-Gaut 94 codon-substitution model coupled with the general time reversible (GTR) model of nucleotide substitution",
   "efv-id":"simulator.substitution_model_pi",
   "frequency-estimator":"frequencies.empirical.corrected.CF3x4",
   "get-branch-length":"",
   "matrix-id":"simulator.substitution_model_Q",
   "models.codon.MG_REV.set_branch_length":{
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   "parameters":{
     "empirical":9,
     "global":{
       "Substitution rate from nucleotide A to nucleotide C":"simulator.substitution_model.theta_AC",
       "Substitution rate from nucleotide A to nucleotide G":"simulator.substitution_model.theta_AG",
       "Substitution rate from nucleotide A to nucleotide T":"simulator.substitution_model.theta_AT",
       "Substitution rate from nucleotide C to nucleotide G":"simulator.substitution_model.theta_CG",
       "Substitution rate from nucleotide C to nucleotide T":"simulator.substitution_model.theta_CT",
       "Substitution rate from nucleotide G to nucleotide T":"simulator.substitution_model.theta_GT"
      },
     "local":{
       "non-synonymous rate":"beta",
       "synonymous rate":"alpha"
      }
    },
   "post-definition":"models.generic.post.definition",
   "q_ij":"models.codon.MG_REV._GenerateRate",
   "reversible":1,
   "set-branch-length":"models.codon.MG_REV.set_branch_length",
   "stop":    {
{"TAA", "TAG", "TGA"} 
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   "time":"models.DNA.generic.Time",
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     "AAC":"N",
     "AAG":"K",
     "AAT":"N",
     "ACA":"T",
     "ACC":"T",
     "ACG":"T",
     "ACT":"T",
     "AGA":"R",
     "AGC":"S",
     "AGG":"R",
     "AGT":"S",
     "ATA":"I",
     "ATC":"I",
     "ATG":"M",
     "ATT":"I",
     "CAA":"Q",
     "CAC":"H",
     "CAG":"Q",
     "CAT":"H",
     "CCA":"P",
     "CCC":"P",
     "CCG":"P",
     "CCT":"P",
     "CGA":"R",
     "CGC":"R",
     "CGG":"R",
     "CGT":"R",
     "CTA":"L",
     "CTC":"L",
     "CTG":"L",
     "CTT":"L",
     "GAA":"E",
     "GAC":"D",
     "GAG":"E",
     "GAT":"D",
     "GCA":"A",
     "GCC":"A",
     "GCG":"A",
     "GCT":"A",
     "GGA":"G",
     "GGC":"G",
     "GGG":"G",
     "GGT":"G",
     "GTA":"V",
     "GTC":"V",
     "GTG":"V",
     "GTT":"V",
     "TAA":"X",
     "TAC":"Y",
     "TAG":"X",
     "TAT":"Y",
     "TCA":"S",
     "TCC":"S",
     "TCG":"S",
     "TCT":"S",
     "TGA":"X",
     "TGC":"C",
     "TGG":"W",
     "TGT":"C",
     "TTA":"L",
     "TTC":"F",
     "TTG":"L",
     "TTT":"F"
    },
   "type":"local"
  },
 "simulator.site.profile":"Constant across sites",
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