Doing quite some DNA analyses lately, I become aware that modern biologists may get drowned by the superfluous amount of tools available. Unless they stick to protocols by peers or literature. And those who are bit on the conservative side, still stick with PAUP of course.
Sometimes the availability of newly developed tools may come in handy though. Francisco Cadiz, a Chilean student working in Brazil, kindly suggested me some literature. One of the papers is a ‘How-to manual’ for the analysis of secondary RNA structures (Schultz & Wolf, 2009) See also http://en.wikipedia.org/wiki/Biomolecular_structure.
Keller et al. (2010) suggest that including these structures into the analyses, the accuracy and robustness is improved in reconstructing phylogenetic trees. Therefore, during the past weekend, I decided to test this myself. It proved not too hard to get this suite of software working. All based on Java and thus problem-free cross-platform. Chapeau developers! The documentation is somewhat crude, but by trial and error I made my own protocol. And the end result was pretty much confirming the results already obtained by other methods.
The danger is of course the dumb application of tools, without understanding of the biological meaning and taxonomical context. That’s always a challenge, especially for modern biologists.
Keller, A., Förster, F., Müller, T., Dandekar, T. Schulz, J. & Wolf, M., 2010. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. – Biology Direct 5: 4 Link:http://www.biology-direct.com/contents/5/1/4 [open access].
Schulz, J. & Wolf, M., 2009. ITS sequence-structure analysis in phylogenetics: A how-to manual for molecular systematics. – Molecular Phylogenetics and Evolution 52: 520-523.