INDELible

[PARTITIONS] block

This block type is used to set root lengths and to choose which models are used with which trees. In addition it is used when simulating multi-partitioned datasets where different sections of the simulated dataset are created with different trees and models.

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Example Usage:

  [PARTITIONS] partitionname [treename name rootlength]

  [PARTITIONS] pM		
    [t1  m1  rootlength1]
    [t2  m2  rootlength2] 
    [t3  b3  rootlength3]
    [t4  m4  rootlength4]
    [t5  b5  rootlength5]

partitionname is used to identify a particular [PARTITIONS] block in the [EVOLVE] block.

treename is the name of any previously defined [TREE] block.

name is the name of any previously defined [MODEL] or [BRANCHES] block.

rootlength is the length of the root sequence that will be generated for this partition.

If using a [BRANCHES] block instead of a [MODEL] block then remember that the trees from the [TREE] and the [BRANCHES] block must match.

Because of this it is NOT permitted to use random trees with [BRANCHES] blocks.

pM is an example of how to define the [PARTITIONS] block when you want to generate multi-partitioned datasets.

The tree, root length and model/branch class can be different in each and every partition and there is no limit on the number of partitions other than that imposed by computer memory.

However the trees must all have the same number of taxa and branch-classes can not be used in the same partition as random trees.