# 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.

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.