CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures

@article{Wolf2005CBCAnalyzerIP,
  title={CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures},
  author={Matthias Wolf and Joachim Friedrich and Thomas Dandekar and Tobias Mueller},
  journal={In silico biology},
  year={2005},
  volume={5 3},
  pages={291-4}
}
The CBCAnalyzer (CBC=compensatory base change) is a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several ct-file formats, and generates a so called "bracket-dot-bracket" format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. CBCDetect counts CBCs in… CONTINUE READING