source: trunk/HELP_SOURCE/source/pa_add.hlp

#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    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           Add species with local optimization

OCCURRENCE      ARB_PARSIMONY/Tree/Add Species to Tree/Add Marked Species + Local Optimization (NNI)
                ARB_PARSIMONY/Tree/Add Species to Tree/Add Selected Species + Local Optimization (NNI)
                ARB_PARSIMONY/Tree/Add Species to Tree/Remove & Add Marked + Local Optimization (NNI)

DESCRIPTION     The functions work like their counterparts described in LINK{pa_quick.hlp}.

                Additionally after all species have been inserted, a LINK{pa_locopti.hlp} takes place.
                This optimization operates on all branches to subtrees containing marked species
                and does not stop at folded groups - regardless
                which settings are selected in LINK{pa_optimizer.hlp}.

WARNINGS        That local optimization will not avoid the need for global tree
                optimization (see LINK{pa_globopti.hlp}).

                Using this function for a bigger number of species (or repeatedly using it), will
                cause your tree to degenerate (see section 'Tree degeneration' in LINK{pa_quick.hlp}
                for more information. What is said there also applies here, the effects are just less worse here).

NOTES           None

EXAMPLES        None

BUGS            No bugs known