Common Methods for Phylogenetic Tree Construction and Their Implementation in R [PDF]
BioengineeringA phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research.
Yujie Zeng
exaly +3 more sources
Ggtree : A serialized data object for visualization of a phylogenetic tree and annotation data
iMeta, 2022 While phylogenetic trees and associated data have been getting easier to generate, it has been difficult to reuse, combine, and synthesize the information they provided, because published trees are often only available as image files and associated data ...
Guangchuang Yu
exaly +2 more sources
Robust Analysis of Phylogenetic Tree Space. [PDF]
Syst Biol, 2022 Phylogenetic analyses often produce large numbers of trees. Mapping trees’ distribution in “tree space” can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different ...
Smith MR.
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
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
Novel metric for hyperbolic phylogenetic tree embeddings. [PDF]
Biol Methods Protoc, 2021 Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of ...
Matsumoto H, Mimori T, Fukunaga T.
europepmc +2 more sources
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
doaj +2 more sources
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
doaj +1 more source
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
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.
Ivica Letunic, P. Bork
semanticscholar +1 more source
Non-binary universal tree-based networks
Journal of Graph Algorithms and Applications, 2022 A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been analyzed in various
Mareike Fischer +2 more
doaj +1 more source