MatOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2.

ABSTRACT:

Motivation

Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the coronavirus disease 2019 (COVID-19) pandemic. One transformative approach, online phylogenetics, aims to incrementally add samples to an ever-growing phylogeny, but there are no previously existing approaches that can efficiently optimize this vast phylogeny under the time constraints of the pandemic.

Results

Here, we present matOptimize, a fast and memory-efficient phylogenetic tree optimization tool based on parsimony that can be parallelized across multiple CPU threads and nodes, and provides orders of magnitude improvement in runtime and peak memory usage compar

SUBMITTER: Ye C 

PROVIDER: S-EPMC9344837 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature