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Last update on 04. Dec 2013 .
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How to get an initial tree

DESCRIPTION

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:

  1. 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);
  2. Select an alignment: <ARB_NT/3rd big Button in top area> (see ´Select an Alignment´)
  3. Start the editor: <ARB_NT/Sequence/Edit marked Sequences> (see ´How to start ARB_EDIT4´)
  4. Align the data (by hand)

Alternatively use ClustalV for aligning (few sequences only):

  • Choose <ARB_NT/ETC/GDE> to activate the GDE extension.
  • Choose <DNARNA/Clustal...> or <Protein/Clustal...> to display the ClustalV window;
  • Click on <help>: read the help and set all parameters
  • Choose an 'alignment' from the Alignment subwindow.
  • Click on <GO>
  • After some time ( 1min - several hours) The aligned data will be shown by the GDE editor.
  • Save the data as: transfer (type: genbank)
  • Quit the GDE program

Reimport the data into ARB_NT:

  • Set the protection level to 6 by clicking ob the <Protection> button and choosing from the displayed menu.
  • Choose the 'Import ... (using GDE/readseq)' item from the 'File' menu to display the 'GDE/File/Import...' window.
  • Type "transfer" to the 'Name of foreign file' subwindow
  • Click on <GO>

WARNING: Sequence names have to contain at least 3 characters.

Reconstruct an initial tree:

  • To get a good tree, you should use different treeing methods.
  • 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.

 

NOTES

None

 

WARNINGS

None

 

BUGS

No bugs known