source: trunk/HELP_SOURCE/source/keeled_groups.hlp

#       main topics:
UP      arb.hlp
UP      glossary.hlp

#       sub topics:
SUB     mode_setroot.hlp
SUB     syncroots.hlp
SUB     mode_group.hlp

# format described in ../help.readme


TITLE           Keeled groups

DESCRIPTION     Taxonomic groups in an unrooted tree(!) can be defined by
                * the branch at which the group is located
                * the direction into which the group points (i.e. which of
                  the 2 subtrees that are connected by this branch does form
                  the defined group)

                In rooted trees the branch location on its own suffices as
                group-defining criteria, if we assume all groups point away from
                the root. This is the way taxonomic groups are handled in most
                software and so did arb (up to version 6.0.6).

                This simple handling of groups was not able to reflect the semantic change
                which is implicitely applied by moving the trees root into a group.

                To solve this problem, arb-7.0 introduced the concept of "keeled groups".

                A keeled group may be interpreted in 2 (semantically equivalent) ways:
                 * the keeled group "points upwards" (i.e. semantically it defines a taxonomic unit containing the two OTHER subtrees starting at its parent-node)
                 * the keeled group "graphically embraces the inverse subset of species" compared with the original unkeeled group

                To indicate keeled groups, their names are prefixed by exclamation
                marks, e.g. shown as '!group' which should be read as "not group";
                this emphasizes the 2nd interpretation given above.

                Example:

                        When the root of the tree is placed somewhere inside a
                        group named 'Bacteria', that group gets keeled over.
                        Its name now gets displayed as '!Bacteria' (should read
                        as "not Bacteria") and the group does embrace the rest
                        of the tree, i.e. "everything but Bacteria".


NOTES           Two groups with different orientation (i.e. a normal and a
                keeled group) may appear at the same inner node.
                This happens e.g. when the original tree had groups defined
                at both subtrees starting directly at root.
                The group name of such a group will be "Normal = !Keeled".

SECTION         Howto 'fix' keeled groups

                It's not possible to export keeled groups into newick files!

                If a tree contains keeled groups, there is a mismatch between
                    - the taxonomy defined by the groups in the tree and
                    - the position of the tree-root.

                One reason for that mismatch is a misplaced tree-root.
                In that case there exists at least one root-position where no
                groups are keeled.
                To find such a position use LINK{mode_setroot.hlp} and
                repeatedly click on any keeled group you spot,
                until they've all disappeared.

                If they won't disappear, the taxonomy of the tree probably is
                not well-defined and has to be resolved manually.
                In that case the following tools may help:

                    - right click onto a keeled group in LINK{mode_group.hlp} to
                      toggle its keeled state,
                    - afterwards use LINK{mode_move.hlp} to correct the position
                      of that group OR
                    - delete a keeled group, if it does no longer fit into the tree.
                      This might e.g. apply after topology changes.

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known