CDMAP/CDVIS: Context-dependent Mutation Analysis Package and Visualization Software

The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) is an automated, modular toolkit used for analysis and visualization of context-dependent mutation patterns (site-specific variation in mutation rate from neighboring-nucleotide effects). The CDMAP algorithm calculates context-dependent mutation rates in chromosomes or replichores, and can generate high-resolution figures to analyze variation in mutation rate across spatiotemporal scales. Output from CDMAP can be integrated into CDVIS, an interactive database for visualizing mutation patterns across multiple taxa simultaneously.