Results 1 to 10 of about 2,045,161 (322)
U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals [PDF]
Plant Diversity, 2023 The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies.
Yi Jin, Hong Qian
doaj +3 more sources
TreeViewer: Flexible, modular software to visualise and manipulate phylogenetic trees [PDF]
Ecology and EvolutionPhylogenetic trees illustrate evolutionary relationships between taxa or genes. Tree figures are crucial when presenting results and data, and by creating clear and effective plots, researchers can describe many kinds of evolutionary patterns.
Giorgio Bianchini +1 more
exaly +3 more sources
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
Indra Rajasingh +1 more
exaly +4 more sources
The agreement distance of unrooted phylogenetic networks [PDF]
Discrete Mathematics & Theoretical Computer Science, 2020 A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection (TBR) and ...
Jonathan Klawitter
doaj +3 more sources
Visualizing incompatibilities in phylogenetic trees using consensus outlines [PDF]
Frontiers in Bioinformatics, 2023 Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis.
Daniel H. Huson +3 more
doaj +2 more sources
PLoS ONE, 2015 Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is
Yi Jin, Hong Qian, Mingjian Yu
doaj +2 more sources
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 ...
Baños, Hector +8 more
openaire +3 more sources
Imputing Phylogenetic Trees Using Tropical Polytopes over the Space of Phylogenetic Trees
Mathematics, 2023 When we apply comparative phylogenetic analyses to genome data, it poses a significant problem and challenge that some of the given species (or taxa) often have missing genes (i.e., data).
Ruriko Yoshida
doaj +1 more source
Computing RF Tree Distance over Succinct Representations
Algorithms, 2023 There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks or cancerous cells in tumor progression trees.
António Pedro Branco +2 more
doaj +1 more source
Trinets encode tree-child and level-2 phylogenetic networks [PDF]
, 2014 Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.
A Dress +27 more
core +11 more sources