source: branches/sina/HELP_SOURCE/source/arb_ntree.hlp

#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      arb.pdf
UP      save.hlp
UP      FAQS.hlp
UP      manual.hlp
UP      help.hlp

#       sub topics:
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

# format described in ../help.readme



TITLE           ARB Main Window

DESCRIPTION     The ARB main window provides access to all available ARB tools for
                analyzing and modifying the data stored in the current ARB 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.

SECTION         ARB menu

        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 or import data.
                Open second window or database.
                Macro recording and playback.

            Species:

                Create, rename, delete, convert, mark, unmark, colorize, search or
                display 'species' and their associated fields. Synchronize species IDs.

            Sequence:

                Create, copy, delete, rename, check, concatenate or modify 'alignments'
                (see LINK{glossary.hlp}). Edit, align, translate or realign sequences.
                Calculate similarity and distance matrices, profiles or filters.

            SAI:

                Copy, delete, rename, convert or combine SAI (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, compare, or modify trees.
                Reconstruct phylogenetic trees.
                Calculate consensus trees.
                Curate taxonomy, fold clades.
                Configure node display (NDS).

            Tools

                A collection of different functions which did not fit well elsewhere.
                All external programs configured via GDE are listed here as well.

            Properties:

                Customize display of windows, trees and data.
                To save these settings for future sessions choose 'Save properties'.

            Many menu entries are linked to explicit help pages.
            To visit such a help page, click the green '?' and
            then the menu entry you'd like to read about.
            See also LINK{help.hlp}.


SECTION Top area

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

            First row:

                Red 'X' button:

                    Quit arb.

                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' (see LINK{glossary.hlp}) and allows
                    switching to another alignment (see LINK{nt_align_select.hlp}).

                'Search' button:

                    Calls LINK{sp_search.hlp}.

                Fourth large button:

                    Displays the ID ('name') of the selected 'species' (see LINK{selected.hlp}) and
                    provides access to the species information window (see LINK{sp_info.hlp}).

            Second row:

                Green '?' button:

                    Click once and then any other element, to see documentation about
                    that element (see LINK{help.hlp}). Click twice to see this page.

                Disk buttons:

                    Save database (quick or full save).

                Circle arrow button:

                    Undo/redo last database transaction.

                Tree display buttons:

                    * First displays radial tree.
                    * Second displays dendrogram tree.
                    * Third displays IRS tree.
                    * Fourth displays just a list of species.

                Editor button:

                    Edit primary and secondary structure (see LINK{e4.hlp}).

                Button below lock:

                    Sets the protection level for user actions in ARB main
                    program (see LINK{security.hlp}).

                Jump button:

                    Scrolls tree display such that the selected species/group
                    gets visible (see LINK{selected.hlp}).

                Marked button:

                    Shows the number of marked species. Click to manage LINK{species_configs.hlp}.

SECTION Mode buttons

        The buttons of the first column of the ARB main 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}).

                The 'ARB main window' formerly has often been referred
                to as 'ARB_NT' or 'ARB_NTREE' window.

EXAMPLES        None

WARNINGS        None

BUGS            Report any bugs:

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