Calculate Branch Lengths

ARB_PARSIMONY/Tree/Calculate Branch Lengths

Calculates branchlengths for the current tree.

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".

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.

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

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´.

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No bugs known