The 'ARB_Parsimony' and 'ARB_NT' windows are similar. 'ARB_
Parsimony' contains a subset of 'ARB_NT' functions and in
addition some tolls for tree reconstruction and evaluation.
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.
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
tree.
-
Stack button: Displays the number of stored tree
topologies
-
Jump button: Displays partial tree within the tree
display area of the 'ARB_NT' window
containing the selected 'species' (see
´Glossary´)
-
HELP button: Displays this help information.
-
First small button: Displays radial tree
-
Second small button: Displays dendrogram
-
+ and - buttons: Define number of stored tree topologies.
Select version to be displayed.
The values after the 'Current Par' and 'Optimal Par' prompts indicate
current and optimal parsimony values for the displayed tree
while moving subtrees manually (see ´MOVE MODE´)
The program works on the selected tree, it does instantly change
the database.
FUNCTIONS:
-
Tree/quick add marked species:
Add all marked species to this tree.
No local rearrangements are performed.
If the species are already in the tree do
nothing.
-
Tree/quick add selected species:
Add the selected species to this tree.
To select a species open the 'Search & Query'
window in ARB Ntree (ARB_NT/species/search);
And select a species.
or: start the editor, make the cursor global
and select a sequence
-
Tree/add marked species:
Quick add plus local rearrangements.
-
Tree/add selected species:
Quick add sel. species plus local rearrangements.
-
Tree/Optimization/Local
Try to find a better tree moving all branches
across one other branch. Does not change
elements in folded subtrees.
-
Tree/Optimization/Global
Try to find a better tree by moving all branches,
over some branches. Does not change
elements in folded subtrees.
Note: This may take a long time. You may stop the
program any time and keep the current best tree.
If you have to answer the question either to
wait or to kill, answer wait.
-
Tree/calculate branch lengths
Does what it says
-
etc.. see ARB Ntree
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