CDMAP/CDVIS: context-dependent mutation analysis package and visualization software.

ABSTRACT: The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) is an automated, modular toolkit used for the analysis and visualization of context-dependent mutation patterns (site-specific variation in mutation rate from neighboring-nucleotide effects). The CDMAP computes context-dependent mutation rates using a Variant Call File (VCF), Genbank file, and reference genome and can generate high-resolution figures to analyze variation in mutation rate across spatiotemporal scales. This algorithm has been benchmarked against mutation accumulation data but can also be used to calculate context-dependent mutation rates for polymorphism or closely related species as long as the input requirements are met. Output from CDMAP can be integrated into CDVIS, an interactive da

SUBMITTER: Patton DL 

PROVIDER: S-EPMC10085751 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature