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//                                                                                 //
//  INDELible V1.03 control file - trees.txt                                       //
//                                                                                 //
//      How to define user trees and how to generate random trees...               //
//                                                                                 //
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[TYPE] NUCLEOTIDE 1	//  nucleotide simulation using algorithm from method 1


[MODEL] mymodel  [submodel]  JC       


  //  You will have already come across user-defined trees in the other examples. 
  //  The following three trees are identical - "white space" of any kind is ignored.

[TREE] t1 ((A:0.1,B:0.1):0.1,(C:0.1,D:0.1):0.1);

[TREE] t2 ( (A:0.1, B:0.1):0.1, (C:0.1, D:0.1):0.1 );

[TREE] t3 
    (             // trees can span any number of lines
      (           // and include any amount of whitespace
        A:0.1,    // including new lines.
        B:0.1    
      ):0.1 ,     // comments within the tree will be ignored.
     (C:0.1,D:0.1):0.1); 

  //  But any tree can also be rescaled to be a certain tree length.
  //  For example the two following trees are identical.

[TREE] T1 ((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);
[treelength] 4.2

[TREE] T2 ((A:0.2,B:0.4):0.6,(C:0.8,D:1.0):1.2);

  
   //  Random rooted & unrooted trees can also be created by INDELible. 
   //  A different tree will be generated for each replicate.
   //  Explanation of these commands follow the examples...

[TREE] tree1
  [unrooted] 10 2.4 1.1 0.2566 0.34  // ntaxa birth death sample mut

[TREE] tree2
  [unrooted] 10 2.4 1.1 0.2566 0.34  // ntaxa birth death sample mut
  [seed] 2381242                     
 
[TREE] tree3
  [rooted] 15 6.7 2.5 0.234 0.31     // ntaxa birth death sample mut
  [treedepth] 0.4

[TREE] tree4
  [rooted] 15 6.7 2.5 0.234 0.31     // ntaxa birth death sample mut
  [treelength] 8

/*
  * Random trees always have taxa names that are numbers. 
    e.g. (1:0.1,2:0.1,(3:0.1,4:0.1):0.1);

  * tree1 and tree2 will be unrooted random trees.
  * tree3 and tree4 will be rooted random trees. 

  * Every time that INDELible is run tree2 will produce the same sequence 
    of random trees, until the number after the [seed] command is changed. 
  * The others (tree1, tree3 and tree4) will always produce different trees.
  * Please note that the [seed] command overrules the [randomseed] 
    command from a [SETTINGS] block, for a random tree.

  * tree4 will produce random trees that are always rescaled to have a tree 
    length of 8, and tree3 will produce random trees that are always rescaled 
    to have a depth (root to tip) of 0.4, whilst the other two (tree1 and 
    tree2) will always produce random trees with different tree lengths/depths.

  * The numbers that come after the [unrooted] and [rooted] commands are 
    the same in both cases.  The first number is the number of taxa 
    (10 for tree1 and tree2, 15 for tree3 and tree4).
  * The next  four are the parameters used in the birth-death process to 
    create the random trees. In order, from left to right, these are the 
    birth-rate, death-rate, sampling fraction and mutation rate. 
    Further details on these parameters can be found in this paper: 
    http://abacus.gene.ucl.ac.uk/ziheng/pdf/1997YangRannalaMBEv14p717.pdf

  * Trees (random or user) that are used during the simulation will be output 
    by INDELible in a file like this.

  * One last point to remember about random trees is that they CANNOT be 
    used when you want the evolutionary model to be permitted to change 
    over the tree. i.e. they CANNOT be used with [BRANCHES] blocks.
   
*/


   //  For a given topology INDELible can also create branch lengths. 
   //  This is done by using the command [branchlengths]
   //  Further explanation of the four examples is given below



[TREE] EQUAL-TREE
  // No branch lengths need to be provided  
  ((((A,B),(C,D)),((E,F),(G,H))),(((I,J),(K,L)),((M,N),(O,P))));
       
  [branchlengths] EQUAL // All branch lengths will be equal
  [treedepth] 0.1       // Root-to-longest-tip distance of 0.1

[TREE] EQUAL-TREE2
  // If branch lengths are provided, they are ignored
  ((((A:0.2,B:0.1):0.4,(C:0.3,D:0.1):0.6):0.1,
  ((E:0.1,F:0.1):0.1,(G:0.2,H:0.1):0.1):0.3):0.1,
  (((I:0.1,J:0.6):0.1,(K:0.1,L:0.1):0.1):0.1,
  ((M:0.4,N:0.1):0.1,(O:0.6,P:0.1):0.1):0.1):0.1); 

  [branchlengths] EQUAL // Again, all branch lengths will be equal
  [treedepth] 0.1       // Root-to-longest-tip distance of 0.1
 
[TREE] ULTRAMETRIC-TREE
  // No branch lengths need to be provided  
  ((((A,B),(C,D)),((E,F),(G,H))),(((I,J),(K,L)),((M,N),(O,P))));

  [branchlengths] ULTRAMETRIC // All branch lengths will be equal
  [treedepth] 0.1             // Root-to-longest-tip distance of 0.1

[TREE] NON-ULTRAMETRIC-TREE
  // No branch lengths need to be provided  
  ((((A,B),(C,D)),((E,F),(G,H))),(((I,J),(K,L)),((M,N),(O,P))));

  [branchlengths] NON-ULTRAMETRIC // All branch lengths will be equal
  [maxdistance] 0.2               // Maximum pairwise distance of 0.2


  
/*
  * [treedepth] 0.1 rescales the tree to have a maximum root-to-tip distance of 0.1
  * After using the [branchlengths] command you should use [treelength] or 
    [treedepth], or [maxdistance] to rescale your tree.

  * [branchlengths] EQUAL will make every branch on the tree equal to 0.1.
  * [branchlengths] NON-ULTRAMETRIC gives every branch a random length between 0 and 1.
  * [branchlengths] ULTRAMETRIC gives every branch a random length between 0 and 1, 
    but will also extend the terminal branches so that the root-to-tip distance is 
    the same for every tip.

  * If the [branchlengths] command is used then the tree toplogy can be specified 
    with or without branch lengths. It does not matter. Any branch lengths will be ignored.
    i.e. the trees EQUAL-TREE and EQUAL-TREE2 will be identical.

  * Examples of the trees produced above can be seen here.
  
  * All trees in the image are rescaled to have a maximum tree-depth of 0.1. 
    This means that the root-to-tip distance for taxon G is equal to 0.1 in all 3 trees.

  * N.B. For ultrametric trees [maxdistance] 0.2 is equivalent to [treedepth] 0.1
    For the non-ultrametric tree they are not the same.
    [maxdistance] 0.2 on the non-ultrametric tree scales the tree such that the sum of 
    the branch lengths in between (in this case) taxons G and N would be 0.2

*/


[PARTITIONS] Pname1  [t1 mymodel 1000]   // tree t1, model mymodel, root length 1000
[PARTITIONS] Pname2  [t2 mymodel 1000]   // tree t2, model mymodel, root length 1000
[PARTITIONS] Pname3  [t3 mymodel 1000]   // tree t3, model mymodel, root length 1000
[PARTITIONS] Pname4  [T1 mymodel 1000]   // tree T1, model mymodel, root length 1000
[PARTITIONS] Pname5  [T2 mymodel 1000]   // tree T2, model mymodel, root length 1000


 
[EVOLVE]     Pname1  10  outputname1     // 10 replicates generated from partition Pname1
             Pname2  10  outputname2     // 10 replicates generated from partition Pname2
             Pname3  10  outputname3     // 10 replicates generated from partition Pname3
             Pname4  10  outputname4     // 10 replicates generated from partition Pname4
             Pname5  10  outputname5     // 10 replicates generated from partition Pname5

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