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Last update on 04. Mar 2022 .

Main topics:

Tree optimization

OCCURRENCE
DESCRIPTION
NOTES
EXAMPLES
WARNINGS
BUGS

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-7.0 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:

'Recursive NNI' will trigger ´Local optimization´
'Heuristic optimizer' will trigger ´Global Optimization´
'Randomize tree' will trigger ´Randomize topology´

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´).