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


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


[MODEL] mA    [submodel] 2.5 2.0  //  M0 with kappa=2.5, omega=2.0
[MODEL] mB    [submodel] 2.5 3.0  //  M0 with kappa=2.5, omega=3.0
[MODEL] mC    [submodel] 2.5 0.5  //  M0 with kappa=2.5, omega=0.5
[MODEL] mD    [submodel] 2.5 1.5  //  M0 with kappa=2.5, omega=1.5
[MODEL] mAB   [submodel] 2.5 2.5  //  M0 with kappa=2.5, omega=2.5
[MODEL] mCD   [submodel] 2.5 0.0  //  M0 with kappa=2.5, omega=0.0
[MODEL] mROOT [submodel] 2.5 1.0  //  M0 with kappa=2.5, omega=1.0

/*
  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

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

/*
  It is important that the order of the taxa and structure of the tree remains
  unchanged between [TREE] and [BRANCHES] blocks (like in this example) because
  taxa names and branch lengths are ignored. i.e. b1a, b1b, b1c are identical to b1.
  but b2a, b2b and b2c are NOT even though the underlying trees are still "correct".


  [BRANCHES] b1a ((A:1.0#mA,B:1.0#mB):1.0 #mAB, (C:1.0 #mC, D:1.0#mD):1.0 #mCD)#mROOT;

  [BRANCHES] b1b ( (#mA, #mB) #mAB,(#mC,  #mD) #mCD)#mROOT;

  [BRANCHES] b1c   
       (   
          (                         // like [TREE] blocks, [BRANCHES] trees 
            A #mA, B#mB             // can contain any amount of white space
          ) #mAB                    // or comments between the first ( and 
        ,                           // the ; at the end.
          (C #mC, D #mD)   
        #mCD)#mROOT;  


  [BRANCHES] b2a ( (B #mB, A#mA) #mAB,(C #mC, D #mD) #mCD)#mROOT;  

  [BRANCHES] b2b ( (C #mC, D #mD) #mCD, (A #mA, B#mB) #mAB)#mROOT;

  [BRANCHES] b2c ( (#mA, #mB) #mAB,(#mD, #mC) #mCD)#mROOT;

*/

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