ArticleSystematic biology2018
Inferring Phylogenetic Networks Using PhyloNet.
Article in Systematic biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 papers.
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Who cites it
143 citing papers in PubMed.
- Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).Cladistics : the international journal of the Willi Hennig Society · 2026Article
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- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- Algebraic Invariants for Inferring 4-Leaf Semi-Directed Phylogenetic Networks.Systematic biology · 2026Article
- When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis.Journal of molecular evolution · 2026Article
- SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.Bioinformatics (Oxford, England) · 2026Article
- Phylogenetic systematics of Juncaceae.American journal of botany · 2026Article
- Phylogenomics unravels the early divergence and diversification in Bignoniaceae.Plant diversity · 2026Article
- Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors.Scientific reports · 2026Article
- PhyloFusion-Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks.Systematic biology · 2026Article
- The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization.Systematic biology · 2026Article
- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Sketch, capture and layout phylogenies.PLoS computational biology · 2025Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Towards a Research Programme Aiming at Causes and Consequences of Reticulate Evolution.Biology · 2025Review
- When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi's paleo-archipelago.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.Plant communications · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
83 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.