The Software Environment and Databases for Ribosomal RNA

The phylogenetic software package ARB (latin: arbor, tree) has been developed for more than 15 years at the Technical University Munich ( www.arb-home.de). It is a comprehensive software package which has primarily been build for ribosomal RNA (rRNA) data, but can be used for any kind of sequence data. The central idea was to arrange a database of sequences and any other additional information according to the phylogenetic relationships of the corresponding organisms. This phylogenetic tree can be visualized on the screen and used for walking through the database by mouse click. Any 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. Tools for importing and exporting different database formats, full text search in any database field, automated alignment of the sequences, online higher order structure check, and various programs for phylogenetic analyses are directly cooperating. Any tool immediately recognizes any change in the database.
A special maximum parsimony approach allows the reconstruction and evaluation of big trees. Furthermore, a powerful sequence editor is implemented which can be used for nucleic acid as well as amino acid sequences. Recent enhancements include an improved system for probe design for fluorescence in situ hybridisations as well as enhanced features for the reconstruction of trees based on protein sequences.

To provide up to date, comprehensive, quality checked and aligned rRNA databases for the users the SILVA project has been set up recently. Check www.arb-silva.de for sequence download and further information.

ARB/SILVA-Workshops are offered on a regular basis in collaboration with the Ribocon GmbH. For details about workshops, comprehensive ARB/SILVA support and an ARB installation CD see www.ribocon.com.