INDELible

[BRANCHES] block

These blocks are used to simulate non-stationary and non-homogenous processes. Different models from different [MODEL] blocks can be specified on different branches of the guide-tree allowing branches to have different models of substitution, indel length distribution, rate heterogeneity, base composition etc.

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Example Usage:

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

  [BRANCHES] b1 ( (A #mA, B#mB) #mAB,(C #mC, D #mD) #mCD)#mROOT;

The easiest way to format a [BRANCHES] block is to cut and paste a tree from a tree block (t1 in this case) and replace the branch lengths with model names from previously defined [MODEL] blocks ( mA, mB ,... etc)

In a similar way that branch lengths are given after a ":" symbol, here model names are given after a "#" symbol.

A model must also be added at the root of the tree also (mROOT here) and will be used in creation of the initial sequence at the root.

Branch lengths and taxa names can be included or omitted at the user's convenience as they are ignored by INDELible - it is only the model names and their position in the parentheses that has any effect. e.g. the following four examples will produce identical results.

  [BRANCHES] b1a ((A:0.1#mA,B:0.1#mB):0.1 #mAB, (C:0.1 #mC, D:0.1#mD):0.1 #mCD)#mROOT;

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

  [BRANCHES] b1c ( (#mA, #mB) #mAB,(#mC,  #mD) #mCD)#mROOT;

  [BRANCHES] b1d 
     ( 
        (                       // 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;

For more examples please see the tutorial section.