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

Main topics:

- ARB: a Short Introduction
- arb.pdf (PDF)

Related topics:

- Trees
- Helix
- Node Display Setup (NDS)
- PT_SERVER: What Why and How
- SAI Sequence Associated Information
- What are Species ?
- Selected Species and Cursor Position
- What is an Alignment ?
- ARB Command Interpreter (ACI)
- What are Marked Species?
- Search and Replace Tool (SRT)

# Glossary

- What do we mean if we talk about ...

## What do we mean if we talk about ...

### ALIGNMENT

Subdatabase containing homologous sequences (different 'alignments' can be stored along with the species information). See ´What is an Alignment ?´ for more information.

### ACI

ARB Command Interpreter. ACI is a simple programing language for calculating special species information (eg. G+C Content..) See ´ARB Command Interpreter (ACI)´.

### EDGE

Branch within a tree defined by nodes

### FIELD

Container for 'species' associated information

### MARKED SPECIES

Marking of 'species' defines the datasubset which is analyzed by the ARB tools. See ´What are Marked Species?´.

### NAMES

There are two kinds of name fields (for species, genes, etc.).

- name
  Identifier for 'species' entries. Should be generated automatically using the name server.
- full_name
  User defined full name of the species,...

### NDS

Node Display Setup: defines information which is displayed at tree nodes.

### NODE

Internal: connects branches of a tree Terminal: free end of branches representing 'species'

### PT_SERVER

Server using a special form of the ARB database for rapid similarity searching (automated alignment, probe design/check)

### SAI

Sequence Associated Information

### SELECTED SPECIES

The 'selected species' is that ONE species which has been selected by using any of the following actions

- ARB_NTREE/Search + click onto one search result
- ARB_MERGE/Transfer species + click onto one search result (here there is one selected species in each of the two involved DBs)
- clicking on the species name in the tree display in ARB_NT
- placing the cursor into the sequence of a species in ARB_EDIT4

The currently selected species will be displayed in the 'Species info window'

### SPECIES

Database entry containing a sequence and associated information. Not necessarily consistent with a taxonomic species

### SRT

Search and Replace Tool allows to search substrings in a string and replace them by another substring (see ´Search and Replace Tool (SRT)´).