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.
NOTE: CBCAnalyzer can be used free of charge in non-commercial projects.
What's New in This Release: [ read full changelog ]
· Added distance matrices for 'halfCBCs' and 'CBCs + halfCBCs'
· Graphical user interface ported to Qt
· CBCAnalyzer now runs on Mac OS X
· The RNAForester format is no longer supported
· CBC Detect now also accepts alignments in extended fasta format