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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Bounds for phylogenetic network space metrics. [PDF]
J Math Biol, 2018 Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex ...
Francis A, Huber KT, Moulton V, Wu T.
europepmc +3 more sources
Phylogenetic network analysis as a parsimony optimization problem. [PDF]
BMC Bioinformatics, 2015 Many problems in comparative biology are, or are thought to be, best expressed as phylogenetic “networks” as opposed to trees. In trees, vertices may have only a single parent (ancestor), while networks allow for multiple parent vertices.
Wheeler WC.
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Phylogenetic diversity and biodiversity indices on phylogenetic networks [PDF]
Mathematical Biosciences, 2018 In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their ...
Fischer, Mareike, Wicke, Kristina
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A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. [PDF]
BMC Bioinformatics, 2016 Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a directed acyclic graph known as a phylogenetic ...
Hejase HA, Liu KJ.
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Extraction of phylogenetic network modules from the metabolic network
BMC Bioinformatics, 2006 Background In bio-systems, genes, proteins and compounds are related to each other, thus forming complex networks. Although each organism has its individual network, some organisms contain common sub-networks based on function.
Goto Susumu +2 more
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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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Rearrangement moves on rooted phylogenetic networks. [PDF]
PLoS Computational Biology, 2017 Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure.
Philippe Gambette +5 more
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Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees [PDF]
Biology Direct, 2009 Background Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and ...
Bernad Lucia +4 more
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Constructing the Simplest Possible Phylogenetic Network from Triplets [PDF]
Algorithmica, 2008 A phylogenetic network is a directed acyclic graph that visualizes an evolutionary history containing so-called reticulations such as recombinations, hybridizations or lateral gene transfers.
L. Iersel, S. Kelk
semanticscholar +3 more sources