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Last update on 25. Nov 2018 .
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Add species with local optimization

OCCURRENCE

ARB_PARSIMONY/Tree/Add Species to Tree/Add Marked Species + Local Optimization (NNI)

ARB_PARSIMONY/Tree/Add Species to Tree/Add Selected Species + Local Optimization (NNI)

ARB_PARSIMONY/Tree/Add Species to Tree/Remove & Add Marked + Local Optimization (NNI)

 

DESCRIPTION

The functions work like their counterparts described in ´Add species without optimizing topology´.

Additionally after all species have been inserted, a ´Local optimization´ takes place. This optimization operates on all branches to subtrees containing marked species and does not stop at folded groups - regardless which settings are selected in ´Tree optimization´.

 

WARNINGS

That local optimization will not avoid the need for global tree optimization (see ´Global Optimization´).

Using this function for a bigger number of species (or repeatedly using it), will cause your tree to degenerate (see section 'Tree degeneration' in ´Add species without optimizing topology´ for more information. What is said there also applies here, the effects are just less worse here).

 

NOTES

None

 

EXAMPLES

None

 

BUGS

No bugs known