/////////////////////////////////////////////////////////////////////////////////////
//                                                                                 //
//  INDELible V1.03 control file - branch2.txt                                     //
//                                                                                 //
//      Using models that change across the tree to implement codon branch models  //
//                                                                                 //
/////////////////////////////////////////////////////////////////////////////////////

  /* 
     Any aspect of a codon model can change over different branches, including:
     kappa, omega, stationary frequencies, indel rates and length distributions.
     However, the number of site classes and the genetic code canNOT change.
     The example below is arbitrary and not meant to be biologically realistic!
  */

[TYPE] CODON 1                    //  codon simulation using algorithm from method 1

[MODEL] mA    
  [submodel]    3.0 1.0  // kappa=3.0, omega=1.0, frequencies equal, no insertions
  [deletemodel] NB 0.2 4 // Pascal deletion length distribution (q=0.2, r=4)
  [deleterate]  0.13     // rate of deletion compared to substitution rate of 1

[MODEL] mB    
  [submodel]    1.0 3.0       // kappa=1.0, omega=3.0, frequencies equal, no deletions
  [insertmodel] POW 1.8 500   // Power-Law insertion length distribution (a=1.8, M=500)
  [insertrate]  0.08          // rate of insertion compared to substitution rate of 1

[MODEL] mAB    
  [submodel]    2.0 2.0  // kappa=2.0, omega=2.0, frequencies different, no indels
  [statefreq]  
    0.016133 0.014626 0.012261 0.019123    //  TTT  TTC  TTA  TTG
    0.008365 0.007583 0.006357 0.009915    //  TCT  TCC  TCA  TCG 
    0.013290 0.012048 0        0           //  TAT  TAC  TAA  TAG
    0.009947 0.009018 0        0.011790    //  TGT  TGC  TGA  TGG
    0.019297 0.017494 0.014665 0.022873    //  CTT  CTC  CTA  CTG 
    0.010005 0.009070 0.007604 0.011859    //  CCT  CCC  CCA  CCG 
    0.015896 0.014410 0.012080 0.018841    //  CAT  CAC  CAA  CAG 
    0.011898 0.010786 0.009042 0.014102    //  CGT  CGC  CGA  CGG 
    0.030728 0.027857 0.023353 0.036422    //  ATT  ATC  ATA  ATG  
    0.015932 0.014443 0.012108 0.018884    //  ACT  ACC  ACA  ACG  
    0.025312 0.022947 0.019236 0.030002    //  AAT  AAC  AAA  AAG  
    0.018945 0.017175 0.014398 0.022456    //  AGT  AGC  AGA  AGG 
    0.024518 0.022227 0.018633 0.029061    //  GTT  GTC  GTA  GTG 
    0.012712 0.011524 0.009661 0.015068    //  GCT  GCC  GCA  GCG  
    0.020196 0.018309 0.015349 0.023938    //  GAT  GAC  GAA  GAG  
    0.015117 0.013704 0.011488 0.017919    //  GGT  GGC  GGA  GGG
               

[MODEL] mC    
  [insertrate]  0.15         // rate of insertion compared to substitution rate of 1
  [submodel]    2.5 0.5      // kappa=2.5, omega=0.5, frequencies equal
  [indelmodel]  POW 2.2 500  // Power Law insertion AND deletion distribution (a=2.2)
  [deleterate]  0.05         // rate of deletion compared to substitution rate of 1

[MODEL] mD    
  [insertmodel] POW 1.9 500  // Power-Law insertion length distribution (a=1.9, M=500)
  [deletemodel] POW 1.7 600  // Power-Law deletion length distribution (a=1.7, M=600)
  [submodel]    2.5 1.5      // kappa=2.5, omega=1.5, frequencies equal
  [indelrate]   0.1          // rate of insertion AND deletion compared to 
                             // substitution rate of 1

[MODEL] mCD   
  [submodel]    2.5 1.0      // kappa=2.5, omega=1.0, frequencies different, no indels
  [insertmodel] POW 1.9 400  // Power-Law insertion length distribution (a=1.9, M=400)
  [insertrate]  0.03         // rate of insertion compared to substitution rate of 1
  [deletemodel] POW 1.7 700  // Power-Law deletion length distribution (a=1.7, M=700)
  [deleterate]  0.17         // rate of deletion compared to substitution rate of 1

[MODEL] mROOT            // Whichever model is defined in the root, that model is only
  [submodel]    0.0 1.0  // used in generation of the root sequence and setting
                         // up the number of site classes across the tree.

/*
  In the same way that lengths of branches are listed after a : symbol in a [TREE]
  block, model names on branches are listed after a # symbol in a [BRANCHES] block. 
  N.B. The structure of the tree & order of taxa is the same (see notes at end of file).
*/

[TREE]     t1 ( (A:1.0, B:1.0):1.0,(C:1.0, D:1.0):1.0);  

[BRANCHES] b1 ( (A #mA, B#mB) #mAB,(C #mC, D #mD) #mCD)#mROOT;  

          
  /* [BRANCHES] blocks are included in [PARTITIONS] blocks in the same way as models */

[PARTITIONS] Pname  [t1 b1 1000]    // tree t1, branchclass b1, root length 1000

[EVOLVE]     Pname  10  outputname  // 10 replicates generated from partition Pname

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

/*
    See extra relevant notes at the end of the file branch.txt here
*/

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