| More docs on the ARB website. See also index of helppages. Last update on 14. Feb 2019 .

Main topics:

- ARB: a Short Introduction
- Glossary
- arb.pdf (PDF)
- Save Database
- FAQ: Frequently Asked Questions
- ARB Manuals

Related topics:

- Trees
- What are Species ?
- What are Genes ?
- SAI Sequence Associated Information
- What is an Alignment ?
- Node Display Setup (NDS)
- NTREE MODES (general info)
- ARB_NTREE keyboard reference
- Using embedded help

# ARB_NT Main Window

- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## 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