ARB Main Window
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.
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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 ´Glossary´). 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 ´Glossary´);
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 ´Using embedded help´.
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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.
Second row:
Green '?' button:
Click once and then any other element, to see documentation about that element (see ´Using embedded help´). 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:
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First displays radial tree.
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Second displays dendrogram tree.
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Third displays IRS tree.
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Fourth displays just a list of species.
Jump button:
Scrolls tree display such that the selected species/group gets visible (see ´Selected species´).
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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.
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The 'ARB main window' formerly has often been referred to as 'ARB_NT' or 'ARB_NTREE' window.
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