/////////////////////////////////////////////////////////////////////////////////////
//                                                                                 //
//  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.
*/

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