CMAPLE: efficient phylogenetic inference in the pandemic era.

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: (1) CMAPLE software, a highly optimized C++ reimplementation of MAPLE with many new features and advancements; and (2) 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 towards better preparedness for future pandemics, offering researchers powerful tools for large-scale pathogen genomic analysis.