source: branches/stable/HELP_SOURCE/oldhelp/arb_ntree.hlp

#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 ID ('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}