********************************************************************************
INDELible V1.03 by Will Fletcher : Simulation began at: Fri Jun 12 01:59:44 2020
********************************************************************************

  Actual Insertion : Deletion Ratio  0.434211 : 0.565789	(Total indel rate = 1)
  Actual average insertion length    3.36364
  Actual average deletion length     3.46512
  Number of insertion events         33
  Number of deletion events          43

  * Block 1 was completed in 0.062497 seconds.

********************************************************************************

  * Simulation completed. Whole batch took: 0.06451 seconds.

INDELible V1.03 Simulations completed at: Fri Jun 12 01:59:44 2020

********************************************************************************


 Original Control File 

-----------------------


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

[SETTINGS]
  [randomseed] 1568746 // seed for random generator so outputs can be checked

[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 20]    // tree t1, branchclass b1, root length 20

[EVOLVE]     Pname  5  outputname  // 5 replicates generated from partition Pname

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