Inferring phylogenies based on compensatory base changes (CBCs). 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.

Before you start working with CBCAnalyzer specify a tree viewer on the preferences dialog. NJPLOT and TreeViewX were tested with this program. If you want to use a different viewer make sure that it accepts the tree file name as a program argument because CBCAnalyzer will start the external viewer from within CBCAnalyzer and passes the tree file name as an argument to the tree viewer.

You can also specify in this dialog if you want to open the resulting trees in one tree viewer instance or to open a tree viewer instance for every single tree by using the checkbox at the bottom of the dialog.

The input text fields where input files are loaded to are not editable by default to prevent the user from invalidating the input data. But if the user knows what he's doing he can enable the edit functionality of the input fields by enabling it via Edit -> Input editable.

CBCAnalyzer Features:
1. Added distance matrices for halfCBCs and CBCs + halfCBCs
2. Graphical user interface ported to Qt
3. CBCAnalyzer now runs on Mac OS X
4. The RNAForester format is no longer supported
5. CBC Detect now also accepts alignments in extended fasta format

Please Note: CBCAnalyzer is freely available for non-commercial use only.

The license of this software is Freeware, you can free download and free use this calculator software.