Abstract: 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 all against all of the
aligned sequences. This is important in detecting species that are
discriminated by their sexual incompatibility. The count (distance) matrix
obtained by CBCDetect is used as input for CBCTree that reconstructs a
phylogram by using the algorithm of BIONJ. In this note we describe the
features of the toolbox as well as application examples. The toolbox provides a
graphical user interface. It is written in C++ and freely available at:
http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de.