## General Information

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 (ct, RNAviz ct or Mac ct), 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. Herewith we count for CBCs in all against all of the aligned sequences, which is important in detecting species, discriminated on 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. The toolbox providing a graphical user interface is written in C++ and freely available for both a Windows, Macintosh, and a Linux environment at:

`http://cbcAnalyzer.bioapps.biozentrum.uni-wuerzburg.de.`

Note that the LINUX version of CBCAnalyzer is still a test version and under development. A program flowchart is given in Figure 1.1.

Figure 1.1: Program flowchart.

Algorithm and program are further described in [1].