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Last update on 25. Nov 2018 .
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Tree optimization

OCCURRENCE

ARB_PARSIMONY/Tree/Tree Optimization

 

DESCRIPTION

This subwindow allows you to configure and access ´Local optimization´, ´Global Optimization´ and ´Randomize topology´.

First you can select whether these functions are applied to the whole tree or whether they only operate on subtrees containing marked species and/or they only operate on visible (i.e. unfolded) parts of the tree.

Note:

The default behavior until arb 6.1 was to operate on marked and visible parts only. Due to several, now fixed bugs it did not strictly restrict to these parts while optimizing.

Then you may trigger the wanted optimization/randomization using the following buttons:


For the 'Heuristic optimizer' click 'Settings' to change ´Kernigham Lin (K.L.) properties´.

 

NOTES

When only optimizing subtrees with marked species, only branches that are drawn in 'Marked' or 'Some marked' color will be modified.

The tree optimizations may as well be called using the 3 tree-modes ´NNI-mode´, ´K.L.-mode´ and ´NNI+KL-mode´. Opposed to using the buttons in the 'Tree optimization' window, these modes normally operate on the clicked subtree only.

After any optimization/randomization the tree will be 'beautified' (see ´Sort Tree Topology´) and branchlengths will be re-calculated (see ´Calculate Branch Lengths´).

Saving the current settings as configuration will save the properties from this window and from the ´Kernigham Lin (K.L.) properties´ window.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known