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Last update on 25. Nov 2018 .
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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 ´Glossary´) associated
                'field' (see ´Glossary´) entries;
                Database searching;
                Automated renaming of 'species'
                Mark and unmark (see ´Glossary´)
        
Sequence:       Create, copy, delete, rename, check, modify
                'alignments' (see ´Glossary´);
                Translate sequences, realign DNA according to
                translated amino acid sequences;
                Edit sequences and 'SAI' (see ´Glossary´).
        
SAI:            Copy, delete, rename, convert Sequence
                Associated Information;
                Calculate consensus and positional variability
Probes:         Probe and Primer design and matching
                Handle 'PT_SERVER' (see ´Glossary´);
        
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 ´Glossary´)
                        and allows switching to another 'Alignment.
        
Fourth large button:    Displays the ID ('name') of the selected
                        'species' (see ´Glossary´) 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
                        ´Glossary´)
        

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 ´Using embedded help´).

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

Report any bugs:

send bug report to devel@arb-home.de