Koetschan et al. (2010) NAR 38:D275-9
Selig et al. (2008) NAR 36:D377-380.
Schultz et al. (2006) NAR 34:W704-7.
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ITS2 3D structure
(Keller et al. 2010)


Chlorophyta hypertree

(Buchheim et al. 2011)
Fig1, Fig2, Fig3, Fig4

Tools

  • 4SALE
    A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing

    • Seibel P.N., Müller T., Dandekar T., Wolf M (2008):
      Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
      BMC Research Notes 1:91
    • Seibel P.N., Müller T., Dandekar T., Schultz J., Wolf M. (2006):
      4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing
      BMC Bioinformatics 7:498
  • ProfDistS
    (Profile-) Distance based phylogeny on sequence-structure alignments

    • 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, pp.:104-117, Hershey, PA, USA: Idea Group, Inc.
    • Friedrich J., Dandekar T., Wolf M, 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., Wolf M. (2004):
      Accurate and Robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
      BMC Evol Biol 4:20
  • Cartoon2Profile
    Converts cartoons as set in FigTree into a ProfDistS compatible profile file

    • Buchheim M.A., Keller A., Koetschan C., Förster F., Merget B., Wolf M. (2011):
      Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: Towards an automated reconstruction of the green algal tree of life
      Plos One 6(2):e16931
    • Merget B., Wolf M. (2010):
      A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data
      BMC Research Notes 3:320
  • CBCAnalyzer
    Inferring phylogenies based on compensatory base changes in rRNA secondary structures

    • Wolf M., Friedrich J., Dandekar T., Müller T. (2005):
      CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures
      In Silico Biol 5:291-294

If you use the database please cite.