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

#       sub topics:
SUB     phylo.hlp

# format described in ../help.readme



TITLE		Starting ARB Parsimony

OCCURRENCE	ARB_NT/Tree/Add species to existing tree/Parsimony ...

DESCRIPTION	ARB Parsimony cannot be used to completely reconstruct new trees.

		Existing trees can be optimized at different levels (depths)
		according to maximum parsimony criteria.

		New sequences (species) can be placed rapidly into an existing
		tree. This can be done without changing that tree or allowing
		optimization at different levels according to maximum parsimony
		criteria including the new information for calculation.

                    The different ways to add species are explained in LINK{pa_quick.hlp}.
                    Standard 'quick add' is available in this menu. To customize behavior
                    or to optimize trees you have to start ARB parsimony in interactive mode.

		Filters for the in- or exclusion of alignment columns
		('ARB_NT/SAI; ARB_NT/Tree/Dist Matrix) can be selected.

                After selecting one of the parsimony items in 'Tree/Add species to existing tree'
		the 'SET PARSIMONY OPTIONS' window appears:

		- Select the tree (to be modified) from the 'Tree:' subwindow.

		- Select an 'alignment' (see LINK{glossary.hlp}) from the
                  'alignment:' subwindow.

		- To select a filter display the 'Select Filter' window pressing
                  the button after the 'Filter:' prompt (see LINK{sel_fil.hlp}).

		- Press the <GO> button to display the 'ARB_PARSIMONY' window.

NOTES		ARB Parsimony will modify the given tree. It might be a good idea to
		create a copy of your tree before you start doing so (see LINK{treeadm.hlp}).

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known