source: branches/profile/HELP_SOURCE/oldhelp/pa_branchlengths.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Calculate Branch Lengths

OCCURRENCE      ARB_PARSIMONY/Tree/Calculate Branch Lengths


DESCRIPTION     Calculates branchlengths for the current tree.


SECTION 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".

SECTION 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.

SECTION 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

SECTION 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