Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances. - Tobias Müller 001; Sven Rahmann; Thomas Dandekar; Matthias Wolf 002 (German Conference on Bioinformatics, 2003)

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. - Joachim Friedrich; Thomas Dandekar; Matthias Wolf 002; Tobias Müller 001 (Bioinform., 2005)

CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. - Matthias Wolf 002; Joachim Friedrich; Thomas Dandekar; Tobias Müller 001 (Silico Biol., 2005)

4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. - Philipp N. Seibel; Tobias Müller 001; Thomas Dandekar; Jörg Schultz; Matthias Wolf 002 (BMC Bioinform., 2006)

The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. - Jörg Schultz; Tobias Müller 001; Marco Achtziger; Philipp N. Seibel; Thomas Dandekar; Matthias Wolf 002 (Nucleic Acids Res., 2006)

Deep Metazoan Phylogeny. - Daniel Gerlach; Matthias Wolf 002; Thomas Dandekar; Tobias Müller 001; Andreas Pokorny; Sven Rahmann (Silico Biol., 2007)

ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. - Matthias Wolf 002; Benjamin Ruderisch; Thomas Dandekar; Jörg Schultz; Tobias Müller 001 (Bioinform., 2008)

The ITS2 Database II: homology modelling RNA structure for molecular systematics. - Christian Selig; Matthias Wolf 002; Tobias Müller 001; Thomas Dandekar; Jörg Schultz (Nucleic Acids Res., 2008)

The ITS2 Database III - sequences and structures for phylogeny. - Christian Koetschan; Frank Förster; Alexander Keller 006; Tina Schleicher; Benjamin Ruderisch; Roland Schwarz 002; Tobias Müller 001; Matthias Wolf 002; Jörg Schultz (Nucleic Acids Res., 2010)