    /////////////////////////////////////////////////////////////////////////////////////
    //                                                                                 //
    //  INDELible V1.03 control file - rates.txt                                       //
    //                                                                                 //
    //      Adding proportion of invariable sites or gamma rate heterogeneity.         //
    //                                                                                 //
    /////////////////////////////////////////////////////////////////////////////////////

    /*
      Nucleotide models are used as an example but the principle is exactly the
      same for amino-acid models. You just add the [rates] command to a model:

        [rates]  pinv  alpha  ngamcat

      This command has no effect in CODON simulations.

      * pinv is the proportion of invariable sites (0<=pinv<=1).
      * alpha is the shape parameter for the gamma distribution (alpha>0).
      * If alpha=0 then there will be no gamma rate variation.
      * ngamcat is the number of categories to use in the discrete gamma approximation.
      * If ngamcat=0 then continuous gamma distribution will be used for rate variation.
      * If the command [rates] is not specified all rates will be constant.

    */

    [TYPE] NUCLEOTIDE 1	//  nucleotide simulation using algorithm from method 1

    [MODEL] mymodel1  [submodel]  JC         //   JC69 with pinv=0.2 and no gamma
                      [rates]     0.2 0 0

    [MODEL] mymodel2  [submodel]  JC         //   JC69 with no proportion invariable,
                      [rates]     0 2 0      //   continuous gamma with alpha=2

    [MODEL] mymodel3  [submodel]  JC         //   JC69 with no proportion invariable,
                      [rates]     0 1 10     //   10 category discrete gamma with alpha=1

    [MODEL] mymodel4  [submodel]  JC         //   JC69 with pinv=0.2
                      [rates]     0.2 0.5 0  //   continuous gamma with alpha=0.5

    [MODEL] mymodel5  [submodel]  JC         //   JC69 with pinv=0.1
                      [rates]     0.1 1.5 5  //   5 category discrete gamma with alpha=1.5

    [TREE] T1  (A:0.1,B:0.1);

    [PARTITIONS] Pname1  [T1 mymodel1 1000]   // tree T1, model mymodel1, root length 1000
    [PARTITIONS] Pname2  [T1 mymodel2 1000]   // tree T1, model mymodel2, root length 1000
    [PARTITIONS] Pname3  [T1 mymodel3 1000]   // tree T1, model mymodel3, root length 1000
    [PARTITIONS] Pname4  [T1 mymodel4 1000]   // tree T1, model mymodel4, root length 1000
    [PARTITIONS] Pname5  [T1 mymodel5 1000]   // tree T1, model mymodel5, root length 1000

    [EVOLVE]     Pname1  10  outputname1     // 10 replicates generated from partition Pname1
                 Pname2  10  outputname2     // 10 replicates generated from partition Pname2
                 Pname3  10  outputname3     // 10 replicates generated from partition Pname3
                 Pname4  10  outputname4     // 10 replicates generated from partition Pname4
                 Pname5  10  outputname5     // 10 replicates generated from partition Pname5