Results 1 to 10 of about 2,017,394 (267)
On Tree Based Phylogenetic Networks [PDF]
arXiv, 2015 A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all tree based. In this work, we present a simply necessary and sufficient condition for tree-based networks and prove ...
Louxin Zhang
arxiv +9 more sources
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. [PDF]
Nucleic Acids Res, 2021 The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone.
Letunic I, Bork P.
europepmc +2 more sources
Rearrangement operations on unrooted phylogenetic networks [PDF]
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
doaj +2 more sources
Harnessing machine learning to guide phylogenetic-tree search algorithms. [PDF]
Nat Commun, 2021 Inferring a phylogenetic tree is a fundamental challenge in evolutionary studies. Current paradigms for phylogenetic tree reconstruction rely on performing costly likelihood optimizations.
Azouri D +4 more
europepmc +2 more sources
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. [PDF]
Nucleic Acids ResThe Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone.
Letunic I, Bork P.
europepmc +2 more sources
Uncertainty in phylogenetic tree estimates [PDF]
Journal of Computational and Graphical Statistics, 2017 Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space.
Bell, Rayna C., Willis, Amy D.
core +4 more sources
On the number of vertices of each rank in phylogenetic trees and their generalizations [PDF]
Discrete Mathematics & Theoretical Computer Science, 2016 We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.
Miklós Bóna
doaj +3 more sources
Folding and unfolding phylogenetic trees and networks [PDF]
arXiv, 2015 Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be 'unfolded' to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain ...
C Semple +17 more
arxiv +4 more sources
The space of ultrametric phylogenetic trees [PDF]
Journal of Theoretical Biology, 2016 The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.
Drummond, Alexei J., Gavryushkin, Alex
core +5 more sources
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. [PDF]
Microbiome, 2016 BackgroundFungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments.
Bolyen, Evan +8 more
core +3 more sources