ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments.
BACKGROUND
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.
Wolf
Matthias
M
Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany. matthias.wolf@biozentrum.uni-wuerzburg.de
Ruderisch
Benjamin
B
Dandekar
Thomas
T
Schultz
Jörg
J
Müller
Tobias
T
D000465:Algorithms; D010802:Phylogeny; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D012313:RNA