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A Universal Phylogenetic Tree [PDF]
The American Biology Teacher, 2001 THIS paper presents a universal phylogenetic tree (Figure 1) suitable for use in high school and college biology classrooms. It is made possible by whole genome sequencing techniques that have been available since the mid 1990s. While it is likely that many of the details of the tree will change in the years ahead as more genome sequences become ...
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Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
BMC Bioinformatics, 2006 Background As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components.
Sun Shiwei +9 more
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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
bioRxiv, 2018 Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine.
Alexey M. Kozlov +4 more
semanticscholar +1 more source
Advanced Science, EarlyView.Lung squamous cell carcinoma (LUSC) is often preceded by sequential premalignant lesions with an increasing probability of malignant progression. Using single‐cell RNA sequencing, the dynamic cellular evolution from normal lung to LUSC tissues is delineated; clonal structure of premalignant and malignant epithelium is reveled; the conversion of immune ...
Baohong Luo +16 more
wiley +1 more source
The space of ultrametric phylogenetic trees
Journal of Theoretical Biology, 2016 Minor changes. This version has been published in JTB.
Alexei J. Drummond, Alex Gavryushkin
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Locating a tree in a phylogenetic network [PDF]
Information Processing Letters, 2010 Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a ...
Charles Semple +2 more
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Measures of clade confidence do not correlate with accuracy of phylogenetic trees. [PDF]
PLoS Computational Biology, 2007 Metrics of phylogenetic tree reliability, such as parametric bootstrap percentages or Bayesian posterior probabilities, represent internal measures of the topological reproducibility of a phylogenetic tree, while the recently introduced aLRT (approximate
Barry G Hall, Stephen J Salipante
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CONSEL: for assessing the confidence of phylogenetic tree selection
Bioinform., 2001 UNLABELLED CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees. The main thrust of the program is to calculate the p-value of the Approximately Unbiased (AU) test using the multi-scale bootstrap ...
Hidetoshi Shimodaira, M. Hasegawa
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Advanced Science, EarlyView.The bottom‐up strategy based on multiomics data is used for the SynCom design, and it successfully inhibited F. nucleatum growth and achieved stable colonization in vivo. In addition, it promoted tryptophan metabolism and secondary bile acid conversion, reduced lipid accumulation, relieved microbiome disorder, decreased inflammatory reaction, and ...
Zhongkun Zhou +11 more
wiley +1 more source
Microorganisms, 2019 Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent “1002 yeast genomes project” has become the most complete catalogue of yeast genetic diversity and a powerful ...
Manuel Villalobos-Cid +6 more
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