Phylogenetic network of infectious bronchitis virus: exploring the impact of migratory birds on viral clustering, evolution, and recombination [PDF]
Veterinary QuarterlyInfectious bronchitis virus (IBV) presents a major threat to global poultry production, necessitating a thorough understanding of its evolutionary relationships for effective control measures.
Yu-Chen Tai, Geng-Ming Hu, Chi-Ming Chen
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Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2 [PDF]
BMC Ecology and Evolution, 2021 Background Rooted phylogenetic networks are used to display complex evolutionary history involving so-called reticulation events, such as genetic recombination.
Rosanne Wallin +3 more
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Multigene phylogeny, phylogenetic network, and morphological characterizations reveal four new arthropod-associated Simplicillium species and their evolutional relationship [PDF]
Frontiers in Microbiology, 2022 Simplicillium species are widely distributed and commonly found on various substrates. A minority of species are associated with arthropods. A spider-associated species Simplicillium araneae, and three insect-associated species, Simplicillium ...
Wanhao Chen +5 more
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Detecting introgression from phylogenetic invariant site patterns using machine learning [PDF]
Applications in Plant SciencesPremise Detecting historical introgression among populations or species from genomic data is a common goal in evolutionary genetics. Most current methods fall into two major categories: network inference and admixture inference.
Patrick F. McKenzie, Deren A. R. Eaton
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A comparison of phylogenetic network methods using computer simulation. [PDF]
PLoS ONE, 2008 We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper ...
Steven M Woolley +2 more
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Detecting network communities: an application to phylogenetic analysis.
PLoS Computational Biology, 2011 This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network ...
Roberto F S Andrade +8 more
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Visualizing incompatibilities in phylogenetic trees using consensus outlines
Frontiers in Bioinformatics, 2023 Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis.
Daniel H. Huson +3 more
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Embedding phylogenetic trees in networks of low treewidth [PDF]
Discrete Mathematics & Theoretical Computer Science, 2023 Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic inference methods ...
Leo van Iersel +2 more
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Genetic Variability of PRRSV Vaccine Strains Used in the National Eradication Programme, Hungary
Vaccines, 2021 Porcine reproductive and respiratory syndrome (PRRS) is a globally spread, highly infectious viral disease. Live, attenuated vaccines against PRRS virus (PRRSV) decrease virus excretion and evoke protective immunity reducing the economic damage caused by
Ádám Bálint +10 more
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The Structure of Level-2 Semi-directed Binary Phylogenetic Networks
Cumhuriyet Science Journal, 2023 Phylogenetic trees describe evolution but due to hybridization events, recombination events or lateral gene transfer, it can be represented as a phylogenetic network.
Nihan Özbaltan
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