Now available ProfDistS:
(Profile-) Distance based phylogeny on sequence-structure alignments


Motivation: Profile Neighbor Joining (PNJ) as implemented in 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 framework that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments - using Profile Neighbor Joining (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

Contact: Tobias Müller, Matthias Wolf.

If you use this program please cite:

Wolf M, Ruderisch B, Dandekar T, Müller T (2008): ProfdistS: (Profile-) Distance based phylogeny on sequence-structure alignments. Bioinformatics 24: 2401-2402

Rahmann S, Müller T, Dandekar T, Wolf M (2006): Efficient and robust analysis of large phylogenetic datasets. In: Advanced Data Mining Technologies in Bioinformatics, Edited by: Hui-Huang Hsu. 104-117 Hershey, PA, USA: Idea Group, Inc.

Friedrich J, Dandekar T, Wolf M and Müller T (2005): ProfDist: A tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics 21: 2108-2109

Müller T, Rahmann S, Dandekar T and Wolf M (2004): Accurate and Robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol Biol 4: 20