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More docs on the ARB website.
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Last update on 06. Sep 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 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)´).