ARB - "A comprehensive software package for phylogenetic analysis"
Dr. Johanna Wesnigk and Prof. Dr. Frank Oliver Glöckner
Max Planck Institute for Marine Microbiology, Celsiusstraße, 128359
Bremen, Germany
Further Reading
Amann, R., W. Ludwig, & K.-H. Schleifer, (1995) Phylogenetic
identification and in situ detection of individual microbial cells
without cultivation. Microbiol. Rev., 59, 43- 69.
Ludwig W., O. Strunk, R. Westram, L. Richter, H. Meier,
Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Foerster, I.
Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S.
Hermann, R. Jost, A. Koenig, T. Liss, R. Luemann, M. May, B.
Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A.
Vilbig, M. Lenke, T. Ludwig, A. Bode and K.-H. Schleifer, (2004)
ARB: a software environment for sequence data. Nucleic Acids
Research, 2004, Vol.32, No.4 363- 37
Ludwig, W. & H.-P. Klenk, (2001) Overview: a phylogenetic
backbone and taxonomic framework for prokaryotic systematics. In:
Garrity, G. (ed.) Bergey's Manual of Systematic Bacteriology (2nd
edn). Springer, New York, pp. 49-65.
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Molecular phylogeny provides a stable framework to address the
diversity of organisms. The understanding of the basic principles of
sequence alignment and phylogenetic tree reconstruction is therefore
essential. To link phylogeny with community composition and structure in
the environment, the application of group- or taxon-specific molecular
probes has become a standard technique over the last years.
To facilitate sequence database maintenance, phylogenetic analysis and
molecular probe design the powerful integrated software package ARB was
developed at the Technical University of Munich. After 10 years of
continuous improvement it has become a standard tool used by experts all
around the world. In order to use the system efficiently, participation in
a training workshop is highly recommended. The workshops give a thorough
introduction into the theoretical background of phylogenetic tree
reconstruction and probe design followed by a "hands-on"
experience on phylogenetic tree making using the freely available software
package ARB.
Description of ARB
ARB (Latin: arbor, tree) is a comprehensive software package originally
developed for ribosomal RNA (rRNA) data. Nowadays, it can is used for any
nucleic- or amino acid sequence data. The central idea is to arrange a
database of sequences and associated descriptive information according to
the phylogenetic relationships of the corresponding organisms. This
phylogenetic tree is visualised and can be used for walking through the
database via simple mouse clicks.
ARB imports raw data and primary structure data from existing sources
like GenBank and EBI. For rRNA data ARB already provides databases with
processed primary structures (aligned sequences). Any additional data
related to the individual sequences can be stored in structured database
fields or linked via local or worldwide networks. Furthermore, to
facilitate in-depth analysis of molecular data a comprehensive selection
of software tools is integrated into ARB. These are controlled via a
common graphical user interface and interact directly with one another as
well as with the database (see Figure 1). Software and start-up databases
are freely available at http://www.arb-home.de.
Technical details and features
1. ARB-Database
The designation and hierarchy of database fields can be customised by
each user. Links to other databases are possible with several levels of
protection facilitating security management. All information stored in the
database, along with the sequence data such as bibliography, user made
entries, or information calculated on-line from the database entries, can
be shown at the terminal nodes of the tree.
Furthermore, all integrated and second-party tools are linked to the
ARB-database. Thus, any changes or rearrangements are immediately known to
all software components without user intervention.
The following tools are integrated:
- Tools for importing and exporting aligned and unaligned nucleic acid
and protein sequences in various database formats;
- Tools for defining sequence profiles and for finding and evaluating
organism or group specific identifiers (probes or primers);
- Database management with full text search in any database field, as
well as complex search options;
- A script language for writing small programs to facilitate recurring
tasks.
2. Sequence editor and alignment
A powerful sequence editor which can be used for nucleic acid and amino
acid sequences allows sequence editing, string search, visualisation of
base pairing, positional variability or likelihood. All colours and
symbols are user defined and separate "align" and
"edit" modes prevent erroneous changes. A special feature for
rRNA sequences is the simultaneous secondary structure editor which helps
the scientist to evaluate probe targets. The following features are
implemented:
- Automated alignment of a sequence according to its next relative
(only for nucleic acids);
- Synchronisation of nucleic acid and amino acid sequence alignments;
- Implemented secondary structure editor (only for rRNA);
- Visualisation of patterns and probes.
3. Phylogenetic reconstruction
For phylogenetic tree making several alternative methods available as
part of the package ranging from simple character counting to a special
maximum parsimony approach that allows the reconstruction and evaluation
of big trees. One prominent feature is the possibility to add sequences to
an existing tree without changing the overall topology. Optimisation of
trees can be applied to the complete or user-selected sub-trees and
intermediate stages can be stored. Various programs for phylogenetic
analyses are directly cooperating within ARB, e.g. some programs of the
PHYLIP package for phylogeny inference are incorporated.
Useful features include:
- Distance matrix, maximum parsimony and maximum likelihood methods;
- Confidence tests (bootstrapping);
- Partial-and full-length sequences can be added to existing trees
without altering the general topology;
- Extended possibilities for tree visualization and optimization.
4. Probe design and evaluation
In just three steps the selection of the target organisms, probe design
and probe match is done and can be visualised. For fluorescence in situ
hybridisation (FISH) the ARB multi-probe software is especially useful. A
peculiarity is the position tree (PT) server, which has to be established
by every user locally. Analyses with the PT-server do not rely upon
aligned sequences and can be used for fast and reliable probe design and
probe check. The advantages of ARB in this respect are:
- Easy graphical selection of target sequences
- Fast and reliable probe design and probe check based on suffix trees
- Graphical visualisation of results in the tree, alignment and
secondary structure
Everybody with an interest in sequence alignment, phylogenetic analysis
and/or probe design and hybridisation should be able to profit from using
ARB. ARB sequence databases are currently available for small subunit
rRNA. Ongoing developments are focusing on:
- Sequence databases for further phylogenetic markers
- A tool for visualisation of accessibility maps
- Further extensions so that ARB can handle complete genomes.
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