On Tree-Based Phylogenetic Networks.

J Comput Biol

Department of Mathematics, National University of Singapore, Singapore .

Published: July 2016


Category Ranking

98%

Total Visits

921

Avg Visit Duration

2 minutes

Citations

20

Article Abstract

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2015.0228DOI Listing

Publication Analysis

Top Keywords

phylogenetic networks
12
tree-based networks
8
networks
6
tree-based
4
tree-based phylogenetic
4
networks large
4
large class
4
class phylogenetic
4
networks trees
4
trees addition
4

Similar Publications

Pathogenic characteristics of Causing Black Root Rot of Carrot.

Plant Dis

September 2025

Institute of Plant Protection, University of Belgrade-Faculty of Agriculture, Department of Phytopathology, Nemanjina 6, Belgrade , Serbia, 11080.

The pathogenic soilborne and postharvest fungus , as newly reported pathogen in Serbia, caused significant disease symptoms on carrot roots and seedlings in inoculation assays. In October 2023, machine-washed and cold-stored carrot roots showed symptoms of black rot of patches and abundant sporulation. The influence of the postharvest treatment of machine washing was confirmed by additional sampling at the production site.

View Article and Find Full Text PDF

Nitrifying communities in activated sludge play a crucial role in biological nitrogen removal processes in municipal wastewater treatment plants. While extensive research has been conducted in temperate regions, limited information is available on nitrifiers in tropical regions. The present study investigated all currently known nitrifying communities in two full-scale municipal wastewater treatment plants in Malaysia operated under low-dissolved oxygen (DO) (0.

View Article and Find Full Text PDF

Casein kinase 1 (CK1) family members are crucial for ER-Golgi trafficking, calcium signalling, DNA repair, transfer RNA (tRNA) modifications, and circadian rhythmicity. Whether and how substrate interactions and kinase autophosphorylation contribute to CK1 plasticity remains largely unknown. Here, we undertake a comprehensive phylogenetic, cellular, and molecular characterization of budding yeast CK1 Hrr25 and identify human CK1 epsilon (CK1ϵ) as its ortholog.

View Article and Find Full Text PDF

Isolation and characterization of Proteus mirabilis bacteriophage T2 and its application.

Microb Pathog

September 2025

Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, Henan province, China; Key Laboratory of Veterinary Biotechnology of Henan Province, College of Veterinary Medicine, Henan Agricultural Unive

Public health problems caused by foodborne illnesses have become increasingly serious. Although it was usually regarded as an opportunistic pathogen causing urinary tract infections in humans, recent years have seen an increasing number of foodborne infections related to P. mirabilis.

View Article and Find Full Text PDF

Genome-wide identification and functional characterization of rapid alkalinization factor 6 as a key peptide regulator of abiotic stress tolerance in Tartary buckwheat.

Plant Sci

September 2025

Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, Institute for Advanced Study, Chengdu University, Chengdu, Sichuan, China. Electronic address:

Rapid alkalinization factors (RALFs) are cysteine-rich signaling peptides in plants that play critical roles in development, immune regulation, and responses to abiotic stress. Despite their importance, the functional characterization of RALF family members in Tartary buckwheat (Fagopyrum tataricum), a nutrient-rich crop known for its remarkable resilience to multiple stresses, remains largely unexplored. In this study, we conducted a comprehensive genome-wide analysis to identify and characterize the FtRALF gene family in Tartary buckwheat, examining their phylogenetic relationships, gene structures, and duplication events.

View Article and Find Full Text PDF