ARB is short for “arbor”, the Latin word for tree. And just like a tree, ARB keeps growing.
The ARB software is targeted at improving the speed and quality of analysis of ribosomal RNA (rRNA) sequence data. From the start, it thus aimed to react to the rapidly increasing number of available rRNA sequence data, for example from environmental samples, and the growing importance of rRNA based identification systems. The entire software along with the databases can be used by scientific community for free.
ARB is the only integrated program package capable of handling up to several millions of rRNA sequences. It is an expert tool, with many advanced features for importing sequence data with accompanying metadata and for both automatic and manual sequence alignment. In ARB, a central database of processed sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. It calculates phylogenetic trees using different treeing models and helps creating consensus trees from several individual tree reconstructions. Since its first version, ARB has spread widely in the scientific community, as underlined by over 6300 citations. “After three major updates between 2005 and 2014, we have moved to a rolling update scheme of ARB with new features constantly built in”, explains chief developer Ralf Westram. “However, after a substantial investment into the code stability it is now time to release a new stable version, which we gave the version number 7.0.” ARB 7.0 includes many new features to improve the handling and curation of sequence data and trees. “We implemented several new functions and complemented and improved existing ones to perfectly meet the needs of the scientific community.” Additionally, there is now the possibility of a Mac portation. The new version was released on September 01, 2021.
“With this new and major update, the analysis of rRNA sequences becomes much more handy. As a result, researchers working in numerous research fields from basic research to biotechnology will benefit substantially”, Wolfgang Ludwig, the founder of ARB, concludes.
The ARB project was started at the Technical University in Munich almost three decades ago in 1992. Since 2014 it is continued by the Department of Molecular Ecology at the Max Planck Institute for Marine Microbiology in Bremen in cooperation with Ribocon GmbH.
From Ribocon GmbH, Bremen, Germany:
Jörg Peplies, Ribocon GmbH, Bremen, Germany
From the Max Planck Institute for Marine Microbiology, Bremen, Germany:
Bernhard Fuchs, Katrin Knittel, Jan Gerken, Frank Oliver Glöckner*, Rudolf Amann, Wolfgang Ludwig
* now at the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, and at the University of Bremen, Germany
Silva, official databases of the software package ARB, is a wide-ranging on-line resource for quality checked and aligned ribosomal RNA (rRNA) sequence data. It provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
LTP stands for “The All-Species Living Tree» Project that was initiated in 2007 as a joint effort between the Molecular Ecology Group at the Max Planck Institute for Marine Microbiology, the Marine Microbiology Group at the IMEDEA, the Department of Microbiology of the TUM and with support of Elsevier, publisher of the journal Systematic and Applied Microbiology. The aim of the project was to generate a highly curated database of all available 16S rRNA gene sequences of type strains of Bacteria and Archaea, as well as to reconstruct the most robust phylogenies using the universal alignment implemented in ARB. Along the almost 15 years collaboration, the LTP has been regularly updated to offer the best tool for genealogical reconstructions for taxonomic purposes.
Highlights from the new release:
1.) curation of phylogenetic trees:
- navigation within trees with hot-keys
- improvements in ARB Parsimony algorithm to reduce “branch attractions” by handling and adding sequences individually
- adding single sequences into an existing tree using the RaxML method
- included a search tool for searching taxonomic groups within and across trees and finding duplicated entries (need for introducing “selected group” similar to “selected species”)
- calculate and search for “average in-group distance” AID
- tree rooting: solved the problem of “keeled groups” when merging and manual curating trees
- configuration of “move group names” was introduced and extended by moving criteria (penalty system)
- comparison of different trees by (1) colorization of different parts of the tree (“topology shading”), (2) synchronized scrolling of two trees in parallel, (3) synchronize tree roots, added display of diagonal tree branches and other tree visualization options
- improved visualization of bootstrap values in the tree
2.) Sequence handling
- flagging sequences in ARB-Sequence Editor setting up to three definable check boxes (“species flags”)
- improved import/export tool with preview function
- corrected “positional variability by parsimony” (PVP) for proteins
- metadata can be transferred and imported individually using predefined sets of rules
- different sequence associated information (SAI) can be logically combined
All functions are documented in the help text files, which are accessible in the respective menus. All help text files are also searchable and available here: http://help.arb-home.de/arb.html and here http://help.arb-home.de/help_index.html