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Last update on 25. Nov 2018 .
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Calculate Branch Lengths

OCCURRENCE

ARB_PARSIMONY/Tree/Calculate Branch Lengths

 

DESCRIPTION

Calculates branchlengths for the current tree.

 

Inner branches

To calculate the lengths of non-terminal branches, branch swapping is used on them.

Branch swapping (aka ´NNI (Nearest Neighbour Interchange)´) is the most atomic operation possible at an inner branch and has as such an effect on the overall costs of the tree (i.e. on the ´Parsimony value´).

That effect is used as branchlength for inner branches.

The branchlength reflects the significance of the branch, i.e.

  • the exact topology around SHORT inner branches has little influence on the overall tree costs, i.e. the calculated topology does most likely NOT reflect the "real phylogentic topology".
  • Opposed, the exact topology around LONG inner branches has big influence on the overall tree costs, i.e. the calculated topology does most likely reflect the "real phylogentic topology".

 

Terminal branches

For terminal branches ARB_PARSIMONY checks how much the overall tree costs changed by adding this species to the tree. The cost gets weighted by the base-count of the species.

i.e.

  • if the species has an identical relative in the tree and is added as neighbor of that relative, the resulting branchlength will be zero.
  • if adding the species increases the tree costs by 50 (mutations) and the species contains 100 bases, the resulting branchlength will be 0.5

This does quite accurately reflect the percentage of residues changed against the rest of the tree.

 

Partial sequences

If you add species with partial sequences as fulllength-species, they might group together in subtrees. To avoid that unwanted behavior, use ´Add marked partial species´.

 

Used terms

  • overall tree costs: minimum number of mutation in the tree
  • base-count: without filtered positions. affected by specified weights.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known