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.
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.
Authors: Roland Schwarz; Philipp N Seibel; Sven Rahmann; Christoph Schoen; Mirja Huenerberg; Clemens Müller-Reible; Thomas Dandekar; Rachel Karchin; Jörg Schultz; Tobias Müller Journal: Nucleic Acids Res Date: 2009-08-06 Impact factor: 16.971
Authors: Christian Koetschan; Frank Förster; Alexander Keller; Tina Schleicher; Benjamin Ruderisch; Roland Schwarz; Tobias Müller; Matthias Wolf; Jörg Schultz Journal: Nucleic Acids Res Date: 2009-11-17 Impact factor: 16.971