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Data on the solution and processing time reached when constructing a phylogenetic tree using a quantum-inspired computer [PDF]
Data in Brief, 2023 Phylogenetic trees provide insight into the evolutionary trajectories of species and molecules. However, because (2n-5)! Phylogenetic trees can be constructed from a dataset containing n sequences, but this method of phylogenetic tree construction is not
Wataru Onodera +4 more
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On the Matrix Condition of Phylogenetic Tree. [PDF]
Evol Bioinform Online, 2020 Phylogenetic comparative analyses use trees of evolutionary relationships between species to understand their evolution and ecology. A phylogenetic tree of n taxa can be algebraically transformed into an n by n squared symmetric phylogenetic covariance matrix C where each element [Formula: see text] in C represents the affinity between extant species ...
Jhwueng DC, O'Meara BC.
europepmc +6 more sources
Characterization of a Branch of the Phylogenetic Tree [PDF]
Journal of Theoretical Biology, 2005 We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a ``tortoise and hare effect'': Those genera with the smallest species death rate are likely to survive much
Stuart Samuel, Gezhi Weng
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Drawing Phylogenetic Trees [PDF]
, 2005 We present linear-time algorithms for drawing phylogenetic trees in radial and circular representations. In radial drawings given edge lengths (representing evolutionary distances) are preserved, but labels (names of taxons represented in the leaves) need to be adjusted, whereas in circular drawings labels are perfectly spread out, but edge lengths ...
Christian Bachmaier +2 more
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Journal of Software for Algebra and Geometry, 2021 We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for ...
Elizabeth Gross +8 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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Biochemical and phylogenetic networks-II: X-trees and phylogenetic trees [PDF]
Journal of Mathematical Chemistry, 2021 The present study, which is a continuation of the previous paper, augments a recent work on the use of phylogenetic networks. We develop techniques to characterize the topology of various X-trees and binary trees of biological and phylogenetic interests. We have obtained the results for various k-level X-trees and phylogenetic networks with variants of
R. Sundara Rajan +5 more
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Information geometry for phylogenetic trees [PDF]
Journal of Mathematical Biology, 2021 AbstractWe propose a new space of phylogenetic trees which we callwald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than existing spaces: in wald space, trees are close if they induce similar distributions on genetic sequence data.
Garba, M. K. +7 more
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Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest. [PDF]
PLoS ONE, 2010 Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages.
Bráulio A Santos +3 more
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