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#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}
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