ArticleMolecular biology and evolution2013
Quartet-net: a quartet-based method to reconstruct phylogenetic networks.
Article in Molecular biology and evolution, 2013. 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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Who cites it
15 citing papers in PubMed.
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- A critical analysis of the current state of virus taxonomy.Frontiers in microbiology · 2023Review
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- Finding Lung-Cancer-Related lncRNAs Based on Laplacian Regularized Least Squares With Unbalanced Bi-Random Walk.Frontiers in genetics · 2022Article
- Screening potential lncRNA biomarkers for breast cancer and colorectal cancer combining random walk and logistic matrix factorization.Frontiers in genetics · 2022Article
- Identifying potential microRNA biomarkers for colon cancer and colorectal cancer through bound nuclear norm regularization.Frontiers in genetics · 2022Article
- Artificial Intelligence Systems for Diagnosis and Clinical Classification of COVID-19.Frontiers in microbiology · 2021Article
- Evaluation of the MGISEQ-2000 Sequencing Platform for Illumina Target Capture Sequencing Libraries.Frontiers in genetics · 2021Article
- Clustering and classification methods for single-cell RNA-sequencing data.Briefings in bioinformatics · 2020Review
- QS-Net: Reconstructing Phylogenetic Networks Based on Quartet and Sextet.Frontiers in genetics · 2019Article
- Identification of Phage Viral Proteins With Hybrid Sequence Features.Frontiers in microbiology · 2019Article
- Genetic Polymorphism Study onBioMed research international · 2018Article
- De Novo Sequencing of aThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2018Article
- Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ-2012 Isolated from Fujian, Southern China.The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2017Article
- Quartet-based methods to reconstruct phylogenetic networks.BMC systems biology · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
Phylogenetic networks can model reticulate evolutionary events such as hybridization, recombination, and horizontal gene transfer. However, reconstructing such networks is not trivial. Popular character-based methods are computationally inefficient, whereas distance-based methods cannot guarantee reconstruction accuracy because pairwise genetic distances only reflect partial information about a reticulate phylogeny. To balance accuracy and computational efficiency, here we introduce a quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. This method can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events. A software called "Quartet-Net" is implemented and available at http://sysbio.cvm.msstate.edu/QuartetNet/.
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