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Bioinformatics Advance Access originally published online on August 21, 2008
Bioinformatics 2008 24(20):2401-2402; doi:10.1093/bioinformatics/btn453
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ProfDistS: (profile-) distance based phylogeny on sequence—structure alignments

Matthias Wolf 1,*, Benjamin Ruderisch 1, Thomas Dandekar 1, Jörg Schultz 1 and Tobias Müller 1,*

1Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: The Profile Neighbor Joining (PNJ) algorithm as implemented in the software ProfDist is computationally efficient in reconstructing very large trees. Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction.

Results: For this ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments—using PNJ with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal also with protein sequences.

Availability: ProfDistS is freely available for non-commercial use for Windows, Linux and MAC operating systems at http://profdist.bioapps.biozentrum.uni-wuerzburg.de.

Contact: tobias.mueller{at}biozentrum.uni-wuerzburg.de; matthias.wolf{at}biozentrum.uni-wuerzburg.de

Associate Editor: Martin Bishop

Received on June 27, 2008; revised on August 19, 2008; accepted on August 19, 2008

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