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Last update on 25. Nov 2018 .
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Local optimization

OCCURRENCE

ARB_PARSIMONY/Tree/Tree Optimization/Recursive NNI

ARB_PARSIMONY/<NNI-mode-button>

 

DESCRIPTION

Locally optimizes (parts of) the current tree.

When called from the 'Tree optimization' window, the optimization is always applied to the whole tree. When called via ´NNI-mode´, it depends on where you click to. The settings from ´Tree optimization´ are used to select the branches to optimize (e.g. marked and/or visible only).

At each such branch, this optimization attempts one NNI (see ´NNI (Nearest Neighbour Interchange)´). If the tree topology improves by that modification, it will be kept. Otherwise it will be undone.

If a better topology has been found, the recursion starts again (and again...) until no NNI further improved the tree (see ´NNI-mode´ for exceptions).

 

NOTES

None

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known