ArticlePLoS computational biology2022
TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Fast and accurate identification of emerging viral reassortment from genome sequences.Nucleic acids research · 2026Article
- PhyloFusion-Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks.Systematic biology · 2026Article
- Sketch, capture and layout phylogenies.PLoS computational biology · 2025Article
- Revealing Reassortment in Influenza A Viruses with TreeSort.Molecular biology and evolution · 2025Article
- Using homologous network to identify reassortment risk in H5Nx avian influenza viruses.PLoS computational biology · 2025Article
- Constrained reassortment and genotype-specific traits shape the evolutionary landscape of galbut virus.Virus evolution · 2025Article
- Concepts and Methods for Predicting Viral Evolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Visualizing and deciphering influenza A(H1N1) pdm09 reassortment in the 2019-23 seasons.Virus evolution · 2025Article
- Concepts and methods for predicting viral evolution.bioRxiv : the preprint server for biology · 2024Article
- Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees.Molecular biology and evolution · 2024Article
- Genetic characterization and pathogenicity in a mouse model of newly isolated bat-originated mammalian orthoreovirus in South Korea.Microbiology spectrum · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.Virus evolution · 2024Article
- Article
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3 authors.
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Abstract
When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.
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