CBCAnalyzer 1.1 beta

CBCAnalyzer 1.1 beta analyzes compensatory base changes (CBCs) in RNA sequences to support studies of molecular evolution, species differentiation, and RNA structure–function relationships.

Key Features:

• CTTransform module: Reads ct, RNAviz ct, and Mac ct file formats and converts RNA secondary-structure representations into a bracket-dot-bracket format.
• CBCDetect module: Counts compensatory base changes (CBCs) across all aligned sequence pairs and produces a count matrix of CBC occurrences.
• CBCTree module: Reconstructs a phylogram from the CBC count matrix using the BIONJ (Biased-Neighbor-Joining) algorithm.
• Interoperability: Generates bracket-dot-bracket output compatible with RNAforester, RNAmovie, and MARNA.
• Implementation: Implemented in C++ for computational processing.

Scientific Applications:

• Molecular evolution: Analysis of CBCs to investigate nucleotide co-variation and evolutionary change in RNA populations.
• Species differentiation: Use of CBC counts to inform species delimitation and differentiation assessments.
• Detection of sexual incompatibility: Identification of CBC patterns that have been associated with species exhibiting sexual incompatibility.
• RNA structure–function studies: Integration of secondary-structure representations with sequence comparisons to study structure–function relationships.
• Phylogenetic inference: Reconstruction and visualization of evolutionary relationships based on CBC-derived distance information.

Methodology:

CTTransform reads ct / RNAviz ct / Mac ct files and outputs bracket-dot-bracket format; CBCDetect counts CBCs across aligned sequence pairs and generates a CBC count matrix; CBCTree builds a phylogram from that count matrix using the BIONJ algorithm.