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: [email protected]; [email protected]