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ARB – A comprehensive Software Package for Phylogenetic Analysis



Location: the Max-Planck-Institute for Marine Microbiology,
Event Type: Training Course
Event Date: 2004-10-04    
End Date: 2004-10-08

Event Description:
ARB – A comprehensive Software Package for Phylogenetic Analysis

Application deadline is 20 June 2004. If the LIMIT on number of participants has not been reached by 20 June, several applicants from one marbef partner will be allowed.
Outline:


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 the community composition and structure in the environment molecular probes have to be designed and applied. Theses tasks demand for a powerful integrated software package. Within the workshops we start with an introduction to the theory of phylogenetic tree reconstruction and probe design followed by an “hands-on” experience on phylogenetic treeing using the freely available software package ARB. ARB has been developed for more than ten years at the Technical University in Munich and is currently used by experts all around the world.


Description of ARB:


ARB (latin: arbor, tree) is a comprehensive software package which had primarily been developed for ribosomal RNA (rRNA) data, but which can be used for any 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 be 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, on line 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. A powerful sequence editor which can be used for nucleic acid as well as amino acid sequences allows sequence editing, string search, visualization of base pairing, positional variability or likelihood as user defined colors and symbols. A secondary structure editor for rRNA sequences is connected to the sequence editor. Nucleic acid and amino acid sequence alignments can be synchronized. Tools for defining sequence profiles, and finding and evaluating organism or group specific identifiers (probes or primers) are included.




Contact email: jharder@mpi-bremen.de

Event programme:
look at http://www.marbef.org/documents/ARBprogram.rtf

Collaborators and organisers:


Website url: http://www.arb-home.de

Registration form: http://www.marbef.org/documents/ARBregistration.rtf

Registration fee: 

Relevant costs that should be taken by MARBEF:  

Possibility for day-care centres (facilities for children): No

MarBEF supported event: Yes

Event within Framework of MARBEF: WP1 - Data Integration

Maximum number of participants: 10

External participants (non MARBEF) allowed: No

Posted by Ward on 2004-04-26 and approved by Webmaster