/////////////////////////////////////////////////////////////////////////////////////
//                                                                                 //
//  INDELible V1.03 control file - multi-partitions.txt                            //
//                                                                                 //
//      Generating multi-partitioned datasets                                      //
//                                                                                 //
/////////////////////////////////////////////////////////////////////////////////////



[TYPE] NUCLEOTIDE 1              // nucleotide simulation using algorithm from method 1

  /*
    Generating multi-partitioned datasets is achieved by simply adding more [..] 
    statements to [PARTITIONS] blocks (see below).  Each partition may contain
    a different [MODEL] or [BRANCHES] block, may have a different length, and may
    use a different tree.  The only restriction is that random trees cannot be used 
    in the same partition as [BRANCHES] blocks and the different trees must all
    have the same number of taxa (with the same taxa names).
  */


[PARTITIONS] Pname1                 // this block only contains a single partition
  [t1 b1 1000]                      // tree t1, branchclass b1, root length 1000

[PARTITIONS] Pname2                 // this block contains multiple partitions
  [t2 m1 100]                       // tree t2, model m1, root length 100
  [t1 b1 500]                       // tree t1, branchclass b1, root length 500
  [t3 m2 200]                       // tree t3, model m2, root length 200
  [t4 m3 350]                       // tree t4, model m3, root length 350
                                    // total root length = 1150

// Models

[MODEL] m1                       // no insertions, no gamma
  [submodel]    HKY 2.5          // HKY with kappa=2.5
  [statefreq]   0.1 0.2 0.3 0.4  // frequencies for T C A G
  [deletemodel] NB 0.2 4         // Pascal deletion distribution (q=0.2, r=4)
  [deleterate]  0.13             // rate of deletion (substitution rate = 1)


[MODEL] m2                       // no deletions, no gamma
  [submodel]    HKY 5.0          // HKY with kappa=5.0
  [statefreq]   0.4 0.3 0.2 0.1  // frequencies for T C A G
  [insertmodel] POW 1.8 500      // Power-Law insertion distribution (a=1.8, M=500)
  [insertrate]  0.08             // rate of insertion (substitution rate = 1)

[MODEL] m3                            //  no indels, continuous gamma
  [submodel]  GTR 0.2 0.4 0.6 0.8 1.2 //  GTR: a=0.2, b=0.4, c=0.6, d=0.8, e=1.2, f=1
  [statefreq] 0.2 0.1 0.4 0.3         //  frequencies for T C A G
  [rates]     0   1.0 0               //  continuous gamma with alpha = 1.0
              
[TREE]     t1 ( (1:1.0, 2:1.0):1.0,(3:1.0, 4:1.0):1.0);  

[BRANCHES] b1 ( (1 #m1, 2#m2) #m3,(3 #m3, 4 #m2) #m1)#m1;  

[TREE]     t2 ( (1:0.3, 2:2.0):0.5,(3:0.4, 4:1.0):0.1);  

[TREE]     t3 ( (3:0.3, 2:2.0):0.5,(1:0.4, 4:1.0):0.1);  

[TREE]     t4 [unrooted] 4 2.4 1.1 0.2566 0.34  // ntaxa birth death sample mut

[EVOLVE]     
  Pname1  10  outputname1           // 10 replicates generated from partition Pname1
  Pname2  10  outputname2           // 10 replicates generated from partition Pname2

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

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

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