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# Calculate Branch Lengths

- OCCURRENCE
- DESCRIPTION
- Inner branches
- Terminal branches
- Partial sequences
- Used terms
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_NT/Tree/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 Neighborhood Interchange) is the most atomic operation possible at an inner branch and has as such an effect on the overall costs of the tree.

### That effect is used as branchlength of the inner branch.

### 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 price is 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 added the species increases the tree costs by 50 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 will group together in distant subtrees.

### But if species are flagged to contain "partial sequences" (this is done by "Add marked partial species"), they are handled differently:

- Each partial species corresponds to one non-partial species
- The partial-species is always inserted "below" the corresponding full-species. Multiple partials may correspond to the same full-species.
- By adding that partial sequence to the tree, the tree costs only raise by the weighted mismatches in the region that overlaps (opposed, non-partial sequences would as well count the missing part as "gap insertions", i.e. the costs for adding a sequence as "partial" are MUCH cheaper).

### Species with partial sequences have the field "ARB_partial" set to 1

## 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