Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.
Sign Up to like & getrecommendations! Published in 2023 at "Systematic biology"
DOI: 10.1093/sysbio/syad031
Abstract: Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools… read more here.
Keywords: matoptimize produces; online phylogenetics; cov phylogenies; maximum likelihood ... See more keywords
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1101/2022.01.12.475688
Abstract: 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 COVID-19 pandemic. One transformative approach, online… read more here.
Keywords: online phylogenetics; tree optimization; phylogenetic tree; optimization ... See more keywords