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Bioinformatics Advance Access originally published online on February 19, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

galaxie—CGI scripts for sequence identification through automated phylogenetic analysis

R. Henrik Nilsson 1,*, Karl-Henrik Larsson 1 and Björn M. Ursing 2

1 Botanical Institute, Göteborg University, Box 461, 405 30 Göteborg, Sweden and 2 Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius v. 35, 171 77 Stockholm, Sweden

Received on August 22, 2003; revised on November 23, 2003; accepted on December 11, 2003
Advance Access Publication February 19, 2004

Motivation: The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis.

Results: Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable.

Availability: A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

Contact: henrik.nilsson{at}botany.gu.se

* To whom correspondence should be addressed.


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