Results 61 to 70 of about 495,194 (321)

Mean and Variance of Phylogenetic Trees [PDF]

Systematic Biology, 2019
Abstract We describe the use of the Fréchet mean and variance in the Billera–Holmes–Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Fréchet mean is comparable to other summary methods, and, despite its stickiness property, is more likely to be binary than the majority-rule ...
Daniel G. Brown, Megan Owen
openaire   +4 more sources

Multidimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition

eLife
Environmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions.
Ming-Qiang Wang, Shi-Kun Guo, Peng-Fei Guo, Juan-Juan Yang, Guo-Ai Chen, Douglas Chesters, Michael C Orr, Ze-Qing Niu, Michael Staab, Jing-Ting Chen, Yi Li, Qing-Song Zhou, Felix Fornoff, Xiaoyu Shi, Shan Li, Massimo Martini, Alexandra-Maria Klein, Andreas Schuldt, Xiaojuan Liu, Keping Ma, Helge Bruelheide, Arong Luo, Chao-Dong Zhu   +22 more
doaj   +1 more source

Confidence Sets for Phylogenetic Trees [PDF]

Journal of the American Statistical Association, 2018
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates their analysis.
openaire   +3 more sources

Visualizing phylogenetic tree landscapes [PDF]

BMC Bioinformatics, 2017
Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies
James C. Wilgenbusch, James C. Wilgenbusch, Wen Huang, Wen Huang, Kyle A. Gallivan   +4 more
openaire   +3 more sources

Treewidth distance on phylogenetic trees [PDF]

Theoretical Computer Science, 2018
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display graph is bounded if the trees are in some formal sense topologically similar.
Steven Kelk, Georgios Stamoulis, Taoyang Wu   +2 more
openaire   +5 more sources

Phylogenetic trees and Euclidean embeddings [PDF]

Journal of Mathematical Biology, 2016
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary ...
Mark Layer, John A. Rhodes
openaire   +4 more sources

Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees

, 2016
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$ and without ...
AD Gordon, AV Aho, C Scornavacca, D Bryant, D Lokshtanov, F Delsuc, J Felsenstein, M Frick, M Ng, M Steel, OR Bininda-Emonds, R Diestel, T Kloks, W Maddison   +13 more
core   +2 more sources

Gut microbiota diversity is prognostic in metastatic hormone receptor‐positive breast cancer patients receiving chemotherapy and immunotherapy

Molecular Oncology, EarlyView.
In this exploratory study, we investigated the relationship between the gut microbiota and outcome in patients with metastatic hormone receptor‐positive breast cancer, treated in a randomized clinical trial with chemotherapy alone or chemotherapy in combination with immune checkpoint blockade.
Andreas Ullern, Kristian Holm, Nikolai Kragøe Andresen, Andreas Hagen Røssevold, Corinna Bang, Bjørn Naume, Johannes R. Hov, Jon Amund Kyte   +7 more
wiley   +1 more source

Darwintree: A Molecular Data Analysis and Application Environment for Phylogenetic Study

Data Science Journal, 2015
DarwinTree (http://www.darwintree.cn) provides an integrated bioinformatics platform that supports all phases of the analytical pathway for phylogenetic study from data collections, phylogenetic tree constructions, visualization of the tree of life, and ...
Zhen Meng, Hui Dong, Jianhui Li, Zhiduan Chen, Yuanchun Zhou, Xuezhi Wang, Shouzhou Zhang   +6 more
doaj   +1 more source

Operads and Phylogenetic Trees

, 2015
We construct an operad $\mathrm{Phyl}$ whose operations are the edge-labelled trees used in phylogenetics. This operad is the coproduct of $\mathrm{Com}$, the operad for commutative semigroups, and $[0,\infty)$, the operad with unary operations corresponding to nonnegative real numbers, where composition is addition.
Baez, JC, Otter, N
openaire   +3 more sources