    /////////////////////////////////////////////////////////////////////////////////////
    //                                                                                 //
    //  INDELible V1.03 control file - indels.txt                                      //
    //                                                                                 //
    //      Adding indels to a nucleotide, amino-acid or codon substitution model      //
    //                                                                                 //
    /////////////////////////////////////////////////////////////////////////////////////

    [TYPE] AMINOACID 2            //  amino-acid simulation using algorithm from method 2

    [MODEL] mymodel1              // this is identical to mymodel2
      [submodel]     WAG
      [insertmodel]  POW 1.7 500  // Power law insertion length distribution (a=1.7, M=500)
      [deletemodel]  POW 1.7 500  // Power law deletion length distribution (a=1.7, M=500)
      [insertrate]   0.1          // insertion rate = 0.1 relative to substitution rate of 1
      [deleterate]   0.1          // deletion rate = 0.1 relative to substitution rate of 1

    [MODEL] mymodel2              // this is identical to mymodel1
      [submodel]     WAG
      [indelmodel]   POW  1.7 500 // Power law insertion/deletion length distribution (a=1.7)
      [indelrate]    0.1          // insertion rate = deletion rate = 0.1
                                  // relative to average substitution rate of 1.

    [MODEL] mymodel3              // insertion/deletion lengths and rates can be different.
      [submodel]     WAG
      [insertmodel]  NB  0.2 4    // Pascal insertion length distribution (q=0.2, r=4)
      [deletemodel]  LAV 1.8 500  // Lavalette deletion length distribution (a=1.8, M=500)
      [insertrate]   0.1          // insertion rate = 0.1 relative to substitution rate of 1
      [deleterate]   0.2          // deletion rate = 0.2 relative to substitution rate of 1

    [MODEL] mymodel4              // insertion/deletion lengths and rates can be different.
      [submodel]     JTT
      [insertmodel]  NB  0.4 1    // Geometric insertion length distribution (q=0.4, r=1)
      [insertrate]   0.1          // insertion rate = 0.1 relative to substitution rate of 1
                                  // deletion rate = 0 relative to substitution rate of 1

    [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

    [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

    /////////////////////////////////////////////////////////////////////////////////////

    /*
       New commands that are relevant to insertions and deletions (indels) are:

       [insertrate]
       Sets the rate of insertion relative to an average substitution rate of 1.

       [deleterate]
       Sets the rate of insertion relative to an average substitution rate of 1.

       [indelrate]
       Sets the rate of insertion AND deletion to be equal. It is equivalent
       to specifying [insertrate] and [deleterate] to have the same value.

       If [insertrate] & [indelrate] are not specified then rate of insertion is zero.
       If [deleterate] & [indelrate] are not specified then rate of deletion is zero.

       [insertmodel]
       Works the same as [indelmodel] but only sets the insertion length distribution.

       [deletemodel]
       Works the same as [indelmodel] but only sets the deletion length distribution.

       [indelmodel]
       This sets the insertion and deletion length distributions at the same time.
       It is equivalent to specifying the commands [insertmodel] and [deletemodel]
       to have the same value.  Options for this command are:

       (1)  [indelmodel]  NB   q  r               //  Negative Binomial Distribution
       (2a) [indelmodel]  POW  a                  //  Zipfian Distribution
       (2b) [indelmodel]  POW  a  M               //  Zipfian Distribution
       (3)  [indelmodel]  LAV  a  M               //  Lavalette Distribution
       (4)  [indelmodel]  USER mylengthmodel.txt  //  User-Defined Distribution

       (1)  This specifies a Pascal (negative binomial) distribution where q is a
            decimal (0<=q<=1) and r is an integer (r>0).

       (2a) This specifies a Zipfian (power law) distribution where a is a decimal (a>1).

       (2b) This also specifies a Zipfian distribution where a is a decimal (a>1).
            However with this format indels longer than length M are not permitted.
            This format is highly recommended for small values of a because
            of the fat-tailed shape of the resulting distribution.

       (3)  This specifies a Lavalette distribution where a is a decimal (a>1) and M is
            an integer (M>1) representing the maximum indel length.

       (4)  This specifies a user-defined indel length model. The file mylengthmodel.txt
            should be in the same directory as the INDELible executable and contain a
            list of relative frequencies (in order of increasing indel length)
            separated by white space, like this.
    */