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The main idea of ARB is to manage database access via a tree.
[ You don't have a tree, but you may access all
species data using 'Species/Search and Query'. ]
There are several ways to construct an initial tree:
Align the sequence data:
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Mark all 'species' (see ´Glossary´)
Choose the item 'Mark all Species'
from the menu 'Species'
of the 'ARB_NT' main window (this program)
(short: ARB_NT/Species/Mark all Species);
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Select an alignment:
<ARB_NT/3rd big Button in top area>
(see ´Select an Alignment´)
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Start the editor:
<ARB_NT/Sequence/Edit marked Sequences>
(see ´How to start ARB_EDIT4´)
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Align the data (by hand)
Alternatively use ClustalV for aligning (few sequences only):
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Choose <ARB_NT/ETC/GDE> to activate the GDE extension.
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Choose <DNARNA/Clustal...> or <Protein/Clustal...> to
display the ClustalV window;
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Click on <help>: read the help and set all parameters
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Choose an 'alignment' from the Alignment subwindow.
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Click on <GO>
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After some time ( 1min - several hours) The aligned
data will be shown by the GDE editor.
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Save the data as: transfer (type: genbank)
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Quit the GDE program
Reimport the data into ARB_NT:
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Set the protection level to 6 by clicking ob the
<Protection> button and choosing from the
displayed menu.
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Choose the 'Import ... (using GDE/readseq)' item
from the 'File' menu to display the
'GDE/File/Import...' window.
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Type "transfer" to the 'Name of foreign file' subwindow
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Click on <GO>
WARNING: Sequence names have to contain at least 3 characters.
Reconstruct an initial tree:
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To get a good tree, you should use different treeing
methods.
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To quickly get an initial tree we recommend to use
neighbour joining:
DNA/RNA or Protein sequence:
Choose the 'Neighbour joining' item from the
'Tree' menu to display the 'NEIGHBOUR
JOINING' window. See help for
setting parameters and tree
reconstruction
Show tree:
Click on the <tree_*> (2nd big rectangular) button in
top area and choose the respective tree
Save everything:
Choose the 'Save Whole Database as' item from the 'File' menu.
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