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#Please insert up references in the next lines (line starts with keyword UP)
UP arb.hlp
UP glossary.hlp
UP mark.hlp
#Please insert subtopic references (line starts with keyword SUB)
#SUB nt_align_select.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 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 LINK{glossary.hlp})
Choose the item 'Mark all Species'
from the menu 'Species'
of the 'ARB_NT' main window (this program)
(normally this is referred as: 'ARB_NT/Species/Mark all Species');
2. Select an alignment:
<ARB_NT/3rd big Button in top area>
(see LINK{nt_align_select.hlp})
3. To align the marked sequences use one of the provided aligners
in 'ARB_NT/Sequence/Align Sequences'
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 for DNA, RNA and Protein sequences:
To start neighbour joining select 'ARB_NT/Tree/Build tree from sequence data/Distance matrix methods/ARB Neighbor Joining',
to display the 'NEIGHBOUR JOINING [ARB_DIST]' window.
Refer to LINK{dist.hlp} for setting parameters of tree reconstruction.
Show the reconstructed tree:
Click on the <tree_*> (2nd big rectangular) button in
top area of ARB_NT 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
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