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

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	subtopic.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		NNI (Nearest Neighbour Interchange)

DESCRIPTION	Searches for a better (more parsimonious) tree by swapping the
                relative positions of subtrees separated by one edge.
                At each inner edge (i.e. at non-leaf edges) three different
                topologies are possible.

                Testing these 3 possible topologies and keeping the best of them,
                is called "Nearest Neighborhood Interchange" (NNI).

SECTION         Possible topologies tested by NNI

                The 3 different topologies checked by performing a NNI are

                (A,B,C = subtrees; R = rest of tree)

                        R           R           R
                         \           \           \ 
                         /\          /\          /\ 
                        A  \        B  \        C  \ 
                           /\          /\          /\ 
                          B  C        A  C        B  A


                Note: there are no other possible topologies containing A,B,C and R!

WARNINGS	None

BUGS		No bugs known