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

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