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Last update on 25. Nov 2018 .
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Randomize topology

OCCURRENCE

ARB_PARSIMONY/Tree/Tree Optimization/Randomize/Random mix tree

 

DESCRIPTION

Randomizes the topology of the current tree.

At each inner branch of the tree, one of the three possible topologies (see ´NNI (Nearest Neighbour Interchange)´) is chosen randomly.

Two parameters are available for mixing:

  • Repeat count
  • Percentage

The 'Repeat count' defines how often each inner edge in the tree may be randomized. Its default value is initialized at startup using the size of the tree. The value is chosen such that each edge may possibly be moved to any other position in the tree.

The 'Percentage' defines the probability to randomize an edge.

 

NOTES

You may already have guessed that this function normally will not optimize your tree :)

Nevertheless: alternately randomizing and optimizing the tree may lead to better topologies.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known