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Last update on 10. Nov 2020 .
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Auto-adjust roots of trees

OCCURRENCE

ARB_NT/Tree/Adjust roots

 

DESCRIPTION

This module allows to synchronize the root position of single or multiple tree topologies.

It provides two different methods:

  • adjust roots of one (or several) trees versus one reference tree.
  • optimize root positions of multiple trees at once to find the minimum combination of pairwise distances.

Use the buttons between the two selection lists to move the trees which should be optimized into the left list.

Select the wanted reference tree in the right list and press the button at the bottom right to adjust the roots of all chosen trees versus the reference tree.

To optimize the root combination of all chosen trees, press the lower left button. This starts a heuristic which tries to find better roots for all selected trees, such that the overall sum of pairwise differences gets minimal.

Opposed to the first method (using a reference tree) the second approach may not necessarily find an optimal distribution of root nodes. Its result may depend on the root positions of the involved trees at startup and therfore using the first method before the second may improve the found result. This method also optimizes the root positions of all trees towards "the center" of all involved species.

 

NOTES

Pressing abort when optimizing root positions of multiple trees, will keep the best so far found positions.

 

EXAMPLES

None

 

WARNINGS

Be aware that changing the position of the trees root does affect the orientation of taxonomic groups. For details refer to ´Keeled groups´.

 

BUGS

No bugs known