#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB    mode_setroot.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE           Auto-adjust roots of trees

OCCURRENCE      ARB_NT/Tree/Adjust roots

DESCRIPTION     This module allows to synchronize the root position of single or
                multiple tree topologies.

                It provides two different methods:

                * adjust roots of one (or several) trees versus one
                  reference tree.
                * optimize root positions of multiple trees at once
                  to find the minimum combination of pairwise distances.

                Use the buttons between the two selection lists
                to move the trees which should be optimized into the left list.

                Select the wanted reference tree in the right list and
                press the button at the bottom right to adjust the roots of
                all chosen trees versus the reference tree.

                To optimize the root combination of all chosen trees, press the
                lower left button.
                This starts a heuristic which tries to find better roots for all
                selected trees, such that the overall sum of pairwise differences
                gets minimal.

                Opposed to the first method (using a reference tree) the second approach
                may not necessarily find an optimal distribution of root nodes.
                Its result may depend on the root positions of the involved trees at startup
                and therfore using the first method before the second may improve the found result.
                This method also optimizes the root positions of all trees towards "the center"
                of all involved species.

NOTES           Pressing abort when optimizing root positions of multiple trees, will
                keep the best so far found positions.

EXAMPLES        None

WARNINGS	Be aware that changing the position of the trees root does affect the
                orientation of taxonomic groups.
                For details refer to LINK{keeled_groups.hlp}.

BUGS            No bugs known
