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

Main topics:

- Using embedded help
- FAQ: Frequently Asked Questions
- Glossary
- Version Info
- ARB: Basic ARB-Shell Commands
- Copyrights
- arb.pdf (PDF)
- ARB change log

Related topics:

- ARB_NT Main Window
- ARB Parsimony
- ARB_EDIT4 - Sequence primary and secondary structure editor
- PT_SERVER: What Why and How
- Save Database
- How to get an initial tree

# ARB: a Short Introduction

- OCCURRENCE
- DESCRIPTION
- HOW TO START
- ARB MODULES
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### General info

## DESCRIPTION

### ARB (ARBor, Latin: tree): A software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction.

### The programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database.

### The ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. The majority of operations can be controlled using the mouse for moving the pointer and the left mouse button for initiating and performing operations

## HOW TO START

### Enter <arb> or <arb filename> to start.

## ARB MODULES

### ARB_DB

A central database of (aligned homologous) sequences and additional information, taken from public databases or supplied by the user, is stored in a (binary or ASCII) file (*.arb).
All ARB tools for database handling and most ARB tools for data analysis act directly upon the database. Any local modifications by individual ARB tools are immediately exported to the database and all other active tools.
The database can be structured according to phylogeny or other user-defined criteria.
Tools for text-oriented database searching are integrated.

### ARB_NT

Phylogenetic trees derived from the data or imported from other sources are displayed within the main window. Different tree topologies, complete trees, and subtrees can be stored and used for "walking" through the database. Database entries can be shown with the tree on the screen or in separate windows. Trees can be used to define subsets of data for display or analysis by other ARB tools.
Publication-ready trees can be produced by shaping the displayed tree topology and printing or exporting the tree to foreign software (TREETOOL [], XFIG []).

### ARB_EDIT4

An editor for the display of sequences and sequence-associated data (masks and filters, consensus sequences, higher-order structure) and basic editing functions is available. This tool allows manual entering of new sequences (with a customized keyboard, if desired); manual modification of alignments; search and replacement of sequence stretches; and printout of data.
Predicted higher-order structure is automatically checked according to a user-provided mask and may be displayed with the sequences by user-definable symbols.

### ARB_ALIGN

The ARB tool for automated sequence alignment searches for the most similar sequences in the database and inserts the new sequence into an existing alignment according to primary and higher-order structural similarity.

### ARB_IMPORT/EXPORT

ARB modules as well as integrated foreign software (GDE [1], READSEQ [2], CONVERTALIGN [3]) can be used for import and export of (subsets of) data in different formats, and for database merging.

### ARB_PROTECTION

Up to six hierarchical protection levels can be individually assigned to database entries to prevent unintended modification or loss of data.

### ARB_NAMES

Unique identifiers are automatically generated for the individual entries and stored with the database. This prevents multiple entries of the same data, and assignment of identical names to different data.

### ARB_PHYL

ARB tools and integrated foreign software (PHYLIP [4], DE SOETE [1], fastDNAml [4]) allow calculation of similarity/distance matrices, conservation profiles, selection masks and phylogenetic tree reconstruction using different treeing approaches.

### ARB_PROBE

Species- and group-specific probes are designed and checked by searching the complete database for unique sequence stretches. Potential probe or target sites are ranked by user-supplied criteria for mismatch weighing.

## NOTES

### Most ARB tools allow user input concerning database structure, data selection, inclusion of additional data, specification of analysis parameters, and design of simple programs for online data analysis. Default values or examples are included in the current release.

### Online help is available for all tools (windows).

## EXAMPLES

### None

## WARNINGS

### !!! The protection level option is only available for sequences in the current release !!!

### !!! The trees provided with the current release are definitely not optimal trees !!! However, they are useful for database walking.

## BUGS

### No bugs known