1. CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era.
- Author
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Ly-Trong, Nhan, Bielow, Chris, Maio, Nicola De, and Minh, Bui Quang
- Subjects
MAXIMUM likelihood statistics ,GENOMICS ,SCIENTIFIC community ,RESEARCH personnel ,MAPLE - Abstract
We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and scalability, here we present two key components: (i) CMAPLE software, a highly optimized C++ reimplementation of MAPLE with many new features and advancements, and (ii) CMAPLE library, a suite of application programming interfaces to facilitate the integration of the CMAPLE algorithm into existing phylogenetic inference packages. Notably, we have successfully integrated CMAPLE into the widely used IQ-TREE 2 software, enabling its rapid adoption in the scientific community. These advancements serve as a vital step toward better preparedness for future pandemics, offering researchers powerful tools for large-scale pathogen genomic analysis. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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