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Last update on 25. Nov 2018 .
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Glossary

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 NAMESERVER (see ´ARB NAMESERVER / Synchronize IDs´).
  • 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 (see ´SAI Administration´)

SELECTED SPECIES

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)´).

ZOMBIES

Zombies are references to former species in a tree, i.e. to species that were in the database when the tree has been calculated, but have meanwhile been deleted (see ´Remove Zombies´)