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

Main topics:

- ARB: a Short Introduction
- Glossary
- What are Marked Species?

Related topics:

- Select an Alignment
- Neighbour joining

# How to get an initial tree

- DESCRIPTION
- NOTES
- WARNINGS
- BUGS

## 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) (normally this is referred as: 'ARB_NT/Species/Mark all Species');
2. Select an alignment: <ARB_NT/3rd big Button in top area> (see ´Select an Alignment´)
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 ´Neighbour joining´ 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