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].