| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary

Related topics:

- NTREE MODES (general info)
- ARB PARSIMONY INTRO ( Filter Weights )
- Store Tree Topologies
- MOVE MODE

# ARB Parsimony

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- BUGS

## OCCURRENCE

### ARB_NT/Tree/Add species to existing tree/Parsimony ...

## DESCRIPTION

### 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

## NOTES

### To create (small) parsimony trees use the phylip program

## EXAMPLES

### None

## BUGS

### None