Calculate Branch LengthsOCCURRENCE
ARB_PARSIMONY/Tree/Calculate Branch Lengths
 

DESCRIPTION
Calculates branchlengths for the current tree.
 

Inner branches
To calculate the lengths of nonterminal branches, branch swapping is used on them.
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 basecount 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 fulllengthspecies, 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

basecount: without filtered positions. affected by specified weights.
 

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