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Tree-Based Unrooted Phylogenetic Networks [PDF]
Bulletin of Mathematical Biology, 2017 Abstract Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph
Francis, Andrew +2 more
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Understanding the tree of life: an overview of tree-reading skill frameworks
Evolution: Education and Outreach, 2019 Diagrammatic depictions of evolutionary relationships play an increasingly important role in scientific and educational literature. Reading evolutionary trees is seen as a major challenge for biologists in learning about evolution and its applications in
Thilo Schramm +2 more
doaj +1 more source
On unrooted and root-uncertain variants of several well-known phylogenetic network problems [PDF]
, 2016 The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized.
Boes, Olivier +4 more
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Nonbinary Tree-Based Phylogenetic Networks [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018 Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events.
Laura Jetten, Leo van Iersel
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Rearrangement operations on unrooted phylogenetic networks
Theory and Applications of Graphs, 2019 Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and ...
Remie Janssen, Jonathan Klawitter
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A new resolution function to evaluate tree shape statistics.
PLoS ONE, 2019 Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed ...
Maryam Hayati +2 more
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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae) [PDF]
PeerJ, 2020 Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single
Tian-Wen Xiao +5 more
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The Fair Proportion is a Shapley Value on phylogenetic networks too
, 2018 The Fair Proportion of a species in a phylogenetic tree is a very simple measure that has been used to assess its value relative to the overall phylogenetic diversity represented by the tree.
Coronado, Tomás M. +2 more
core +1 more source
eLifeEnvironmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions.
Ming-Qiang Wang +22 more
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Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs
, 2017 We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide ...
Bodily, Paul M. +7 more
core +1 more source