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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