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

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SUB	mode.hlp
SUB	arb_pars_init.hlp
SUB	ap_stack.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		ARB Parsimony

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

DESCRIPTION	The 'ARB_Parsimony' and 'ARB_NT' windows are similar. 'ARB_
		Parsimony' contains a subset of 'ARB_NT' functions and in
		addition some tolls for tree reconstruction and evaluation.

	Clicking on the prompts in the horizontal menu bar in the upper part of
        the window displays the corresponding submenus. The submenus are
        also available using keyboard shortcuts by pressing the meta and
        a letter key indicated in the main menu bar by underlining.

	The buttons of the area between the main menu bar and the tree display
        area (from left to right) ('called top area'):

		First large button:	Displays the name of the current
					tree.

		Stack button:		Displays the number of stored tree
					topologies

		Jump button:		Displays partial tree within the tree
					display area of the 'ARB_NT' window
					containing the selected 'species' (see
					LINK{glossary.hlp})

		HELP button:		Displays this help information.

		First small button:	Displays radial tree

		Second small button:	Displays dendrogram

		+ and - buttons:	Define number of stored tree topologies.
					Select version to be displayed.

	The values after the 'Current Par' and 'Optimal Par' prompts indicate
        current and optimal parsimony values for the displayed tree
        while moving subtrees manually (see LINK{mode_move.hlp})

        The program works on the selected tree, it does instantly change
        the database.

		FUNCTIONS:

			Tree/quick add marked species:

				Add all marked species to this tree.
				No local rearrangements are performed.
				If the species are already in the tree do
				nothing.

			Tree/quick add selected species:

				Add the selected species to this tree.
				To select a species open the 'Search & Query'
				window in ARB Ntree (ARB_NT/species/search);
				And select a species.
				or: start the editor, make the cursor global
				and select a sequence

			Tree/add marked species:

				Quick add plus local rearrangements.

			Tree/add selected species:

				Quick add sel. species plus local rearrangements.

			Tree/Optimization/Local

				Try to find a better tree moving all branches
				across one other branch. Does not change
				elements in folded subtrees.

			Tree/Optimization/Global

				Try to find a better tree by moving all branches,
				over some branches. Does not change
				elements in folded subtrees.
				Note: This may take a long time. You may stop the
				program any time and keep the current best tree.
				If you have to answer the question either to
				wait or to kill, answer wait.

			Tree/calculate branch lengths

				Does what it says

			etc.. see ARB Ntree




NOTES		To create (small) parsimony trees use the phylip program


EXAMPLES        None


BUGS		None
