ArticleBioinformatics (Oxford, England)2022
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 35 citations in OpenAlex.
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- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Practical phylogenetic usage of theoretical advances in distance-based tree learning.BMC bioinformatics · 2026Article
- Predicting the antigenic evolution of seasonal influenza viruses using phylogenetic convergence.bioRxiv : the preprint server for biology · 2026Article
- Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.Nature methods · 2026Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.Nature methods · 2026Article
- larch: mapping the parsimony-optimal landscape of trees for directed exploration.bioRxiv : the preprint server for biology · 2025Article
- UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis ofmedRxiv : the preprint server for health sciences · 2025Article
- Epidemic-induced local awareness behavior inferred from surveys and genetic sequence data.Nature communications · 2025Article
- The lives of cells, recorded.Nature reviews. Genetics · 2025Review
- Phylogenetic Tree Instability After Taxon Addition: Empirical Frequency, Predictability, and Consequences For Online Inference.Systematic biology · 2025Article
- Analysis-ready VCF at Biobank scale using Zarr.bioRxiv : the preprint server for biology · 2025Article
- Analysis-ready VCF at Biobank scale using Zarr.GigaScience · 2025Article
- CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics.GigaByte (Hong Kong, China) · 2025Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.bioRxiv : the preprint server for biology · 2024Article
- MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.Systematic biology · 2024Article
- Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.Molecular biology and evolution · 2024Article
- Robust expansion of phylogeny for fast-growing genome sequence data.PLoS computational biology · 2024Article
- Ranked Subtree Prune and Regraft.Bulletin of mathematical biology · 2024Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
motivationPhylogenetic 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.
resultsHere, 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 compared to existing state-of-the-art methods. We have developed this method particularly to address the pressing need during the COVID-19 pandemic for daily maintenance and optimization of a comprehensive SARS-CoV-2 phylogeny. matOptimize is currently helping refine on a daily basis possibly the largest-ever phylogenetic tree, containing millions of SARS-CoV-2 sequences. AVAILABILITY AND IMPLEMENTATION: The matOptimize code is freely available as part of the UShER package (https://github.com/yatisht/usher) and can also be installed via bioconda (https://bioconda.github.io/recipes/usher/README.html). All scripts we used to perform the experiments in this manuscript are available at https://github.com/yceh/matOptimize-experiments. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.