#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      pars.hlp
UP      mode_nni.hlp
UP      mode_optimize.hlp

#       sub topics:
#SUB     subtopic.hlp

# format described in ../help.readme


TITLE		K.L. optimization

OCCURRENCE	ARB_PARSIMONY/<K.L.-mode-button>
                as part of LINK{pa_globopti.hlp}

DESCRIPTION	Searches for a better (more parsimonious) tree by swapping
		subtrees which are separated by many edges.

                Not all possible topologies are tested here, because there
                are far too many (see LINK{kernlin.hlp} for details).

                Instead the K.L. optimizer selects several "paths" through the tree (we call
                this selection 'path reduction') and follows only those paths, while performing
                NNIs (see LINK{nni.hlp}) along it's way.

                These NNIs are even attempted, when single NNIs degrade the quality of the topology.
                If some intermediate or the final NNI (which is by default done 15 edges away from
                the edge starting from) leads to an improvement of the tree, the topology change
                is kept. Otherwise all changes are undone and the next path will be attempted.

                The default maximum path length of 15 and several parameters concerning the path reduction
                may be configured in LINK{kernlin.hlp}.

NOTES		The K.L. optimization occurs as step 2 of LINK{pa_globopti.hlp}.

                It can be called directly using LINK{mode_kernlin.hlp}.

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known
