Journal Article

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

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

in Bioinformatics

Volume 24, issue 20, pages 2401-2402
Published in print October 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btn453
ProfDistS: (profile-) distance based phylogeny on sequence—structure alignments

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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@biozentrum.uni-wuerzburg.de; matthias.wolf@biozentrum.uni-wuerzburg.de

Journal Article.  1053 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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