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

#Please insert subtopic references  (line starts with keyword SUB)
SUB	trees.hlp
SUB	species.hlp
SUB	genes.hlp
SUB	extended.hlp
SUB	alignment.hlp
SUB	props_nds.hlp
SUB	mode.hlp
SUB	nt_keys.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_NT Main Window

DESCRIPTION	'ARB_NT' is the main window for the current ARB database and
		provides access to all ARB tools for analyzing and modifying
		this database via menus or buttons.

		The tree shown within the tree display area can be used to walk
		through the database, to structure it according to phylogeny,
		and to display any information stored within the database at its
		nodes.

	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.

		File:		Save the database, export and import data.

		Species:	Display, create, rename, delete, convert
				'species' (see LINK{glossary.hlp}) associated
				'field' (see LINK{glossary.hlp}) entries;
				Database searching;
				Automated renaming of 'species'
				Mark and unmark (see LINK{glossary.hlp})

		Sequence:	Create, copy, delete, rename, check, modify
				'alignments' (see LINK{glossary.hlp});
				Translate sequences, realign DNA according to
				translated amino acid sequences;
				Edit sequences and 'SAI' (see LINK{glossary.hlp}).

		SAI:		Copy, delete, rename, convert Sequence
				Associated Information;
				Calculate consensus and positional variability

                Probes:         Probe and Primer design and matching
				Handle 'PT_SERVER' (see LINK{glossary.hlp});

		Tree:		Copy, delete, import, export, print trees;
				Modify tree display;
				Calculate similarity/distance matrices,
				profiles, filters;
				Reconstruct phylogenetic trees.

		Properties:	Customize display of windows, trees and data.
				To save the settings choose the 'Save Defaults'
				item from the 'File' menu.

		ETC:		A collection of different functions.
				Use external programs via GDE.


	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
					database and allows you [or "the user"] to save it.

		Second large button:	Indicates the name of the current tree
					and allows selection of the tree to be
					displayed.

		Third large button:	Indicates the name of the current
					'alignment' (subdatabase; see LINK{glossary.hlp})
                                        and allows switching to another 'Alignment.

		Fourth large button:	Displays the name of the selected
					'species' (see LINK{glossary.hlp}) and
					provides access to the database search
					tools.

		Protection button:	Sets the protection level for the
					current 'alignment'

		HELP button:		Displays this help information.

		First small button:	Displays radial tree

		Second small button:	Displays dendrogram

		Third small button:	Sequence editing

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

	The buttons of the first column of the 'ARB_NT' window are used to
        select different modes for editing and modifying the current tree shown
        in the tree display area.


NOTES		Online help is available for all menu items and buttons (see
		LINK{help.hlp}).

EXAMPLES	None

WARNINGS	None

BUGS		Report any bugs:

                       send bug report to LINK{devel@arb-home.de}
