Results 71 to 80 of about 281,835 (164)

Using Plant DNA Barcodes and Functional Traits to Assess Community Assembly of Quercus Forests at Different Scales in the Semiarid Loess Plateau of China

Ecology and Evolution
Trait and evolutionary differences among coexisting species are increasingly used to comprehend the processes shaping communities. However, they do not consistently yield congruent insights due to methodological limitations and scale dependence ...
YongFu Chai, TingTing Tian, Luyao Wang, Junxin Wei, Yao Xu, Peiliang Liu, Chengcheng Xiang, Ming Yue   +7 more
doaj   +1 more source

Reliable estimation of tree branch lengths using deep neural networks.

PLoS Computational Biology
A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree,
Anton Suvorov, Daniel R Schrider
doaj   +1 more source

Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
doaj   +1 more source

Phylogeny-informed random forests for human microbiome studies

Microbiology Spectrum
Random Forest is a widely used tree-based ensemble learning algorithm that efficiently captures complex nonlinear relationships and higher-order feature interactions with no distributional assumptions to be satisfied.
Hyunwook Koh
doaj   +1 more source

Fusang: a framework for phylogenetic tree inference via deep learning. [PDF]

Nucleic Acids Res, 2023
Wang Z, Sun J, Gao Y, Xue Y, Zhang Y, Li K, Zhang W, Zhang C, Zu J, Zhang L.   +9 more
europepmc   +1 more source

Phylogenetic degrees for claw trees

Journal of Combinatorial Theory, Series A
Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining the algebraic degrees of the phylogenetic varieties coming from these models.
Rodica Andreea Dinu, Martin Vodicka
openaire   +3 more sources

Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data. [PDF]

Genome Res, 2023
Zhang L, Bass HW, Irianto J, Mallory X.
europepmc   +1 more source

Dissecting discordance of mitochondrial and nuclear phylogenetic trees in insects

Crop Health
The mitochondrial and nuclear genomes present distinct inheritance and genomic structural characteristics. Although both genomes have been widely used for phylogenetic tree reconstruction, topological discordances between trees inferred from ...
Xianfeng Mi, Guo-Zheng Ou, Yixiao Zhu, Xing-Xing Shen   +3 more
doaj   +1 more source

Robust Analysis of Phylogenetic Tree Space. [PDF]

Syst Biol, 2022
Smith MR.
europepmc   +1 more source

GPTree Cluster: phylogenetic tree cluster generator in the context of supertree inference. [PDF]

Bioinform Adv, 2023
Koshkarov A, Tahiri N.
europepmc   +1 more source