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UP      glossary.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Multifurcate tree

OCCURRENCE      ARB_NT/Tree/Modify branches/Multifurcate

DESCRIPTION     Trees constructed by treeing algorithms often suggest a precision
                which does in fact not exist in reality. To make it impossible to draw wrong
                conclusions from your tree, you might consider to multifurcate specific
                branches, especially such with low bootstrap values.

                In the 'Multifurcate tree' window you can restrict which branches shall be
                multifurcated by specifying lower limits for
                  * bootstrap and/or
                  * branchlength.

                All branches below the specified and selected limits will be multifurcated,
                i.e. their length will be set to zero and their bootstrap value (if any) will be
                removed by clicking on the 'Multifurcate' button.

                This is only applied to terminal (i.e. leaf) branches, if 'Also apply to
                terminal branches' is checked.

                The algorithm does not change the sum of the branchlengths of the tree (which is
                a measure for the phylogenetic distance between all tree members).
                To achieve that the algorithm distributes the former branchlength of each removed
                branch to its directly adjacent neighbour branches.

                Removing the branch C from this example tree

                            B
                         +----
                      A  |
                     ----+       D
                         |    +----
                         +----|
                            C +----
                                 E

                will result in a multifurcated tree

                             b
                          +-----
                      a   |
                     -----+  d
                          +-----
                          |
                          +-----
                             e


                with modified branchlengths, where

                     SUM(a,b,d,e) = SUM(A,B,C,D,E)

                The distribution is performed proportionally to the length of the target branches
                of the distribution, i.e. longer branches receive more of the distributed
                length than shorter branches.

                Branches with zero branchlength are never changed, as they already represent (and
                will remain) multifurcations. Instead the length is distributed to the next
                adjacent branches beyond the multifurcation. This is true for existing and for
                just created multifurcations.

                The distribution simultaneously takes place at all affected branches,
                always considering the former branchlengths for calculating the proportion
                and avoiding summarizing effects at repeatedly affected branches (i.e. at branches
                with multiple removed neighbour branches)

NOTES           The sum of all branchlengths in a tree modified with 'Multifurcate tree' will
                remain constant (disregarding possible numerical problems and the abnormal case that
                ALL branches get multifurcated).

                See LINK{branch_analysis.hlp} on HOWTO calculate the sum of all
                branchlengths of a tree.

EXAMPLES        To see how the distribution works for single branches, display a small tree
                with only a few species, select the MULTIFURCATE MODE (see LINK{mode_length.hlp})
                and drag some branches to scale their length.

WARNINGS        Selecting none of the limits will remove the lengths from all branches and the sum
                of branchlengths of the tree will change to zero. This
                option makes no sense at all and is only provided for your relief in case you're
                fed up with topologies and feel the urgent need to easily get rid of one of them.

BUGS            No bugs known