//                                                                                 //
//  INDELible V1.03 control file - branchsite.txt                                  //
//                                                                                 //
//      Implementing codon branch-site models using the [BRANCHES] command         //
//                                                                                 //

    Branch-site models are defined just like branch models except the individual models 
    have more site classes (i.e. omega categories). Different models can be defined for 
    every branch on the tree if desired and there is no limit on the number of site 
    classes that can be defined. However, it is important to remember that the number 
    of site classes (and their relative proportions) cannot change on the tree.

    Also, the genetic code is not permitted to change but everything else is, including:
    kappa, omega, stationary frequencies, and the indel rates and length distributions. 
    The examples below will only show omega changing amongst models.

[TYPE] CODON 1                    

  /* Notice that the number of classes and proportions do not change below. */

                   // Kap p0  p1  w0  w1  w2     (p2=1-p1-p0=0.5) 
[MODEL] x1 [submodel] 2.5 0.2 0.3 0.0 0.5 1.0 
[MODEL] x2 [submodel] 2.5 0.2 0.3 0.1 1.0 3.0  
[MODEL] x3 [submodel] 2.5 0.2 0.3 0.2 2.0 6.0  
     Like before, to get a correctly formatted [BRANCHES] block from a [TREE] block
     simply cut and paste the tree and change the branch lengths to model names.
     The stationary frequencies of the model at the root are used to generate the
     root sequence and this model defines the number of site categories used.

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

[BRANCHES] b1  ((A #x1, B #x2) #x1,(C #x1, D #x3) #x1)#x1;  

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

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


   If (instead of model names) we write omega values after the # symbol
   on branches in a tree then the branches class b1 above is the same 
   as saying that different sites will evolve according to the following:
      0.2   ( (A #0.0, B#0.1) #0.0,(C #0.0, D #0.2) #0.0); 
      0.3   ( (A #0.5, B#1.0) #0.5,(C #0.5, D #2.0) #0.5); 
      0.5   ( (A #1.0, B#3.0) #1.0,(C #1.0, D #6.0) #1.0); 

    i.e. 20% of sites will evolve with omega=0 except on the branch to B 
           where omega = 0.1 and on the branch to D where omega = 0.2,
         30% of sites will evolve with omega=0.5 except on the branch to B 
           where omega = 1 and on the branch to D where omega = 2,
         50% of sites will evolve with omega=1.0 except on the branch to B 
           where omega = 3 and on the branch to D where omega = 6.

    A format similar to above is used by Evolver in the PAML suite for simulating
    under branch-site codon models. However, the method implemented in INDELible 
    also allows for kappa, stationary frequencies and indel parameters to change too.
    Also, see extra relevant notes at the end of the file branch.txt here

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