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Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Evolutionary Phylogenetic Networks: Models and Issues
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Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
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Two Results on Distances for Phylogenetic Networks
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Folding and unfolding phylogenetic trees and networks
inferredcites →https://doi.org/10.1016/j.tig.2014.07.007openalex-snapshot
Toward a new history and geography of human genes informed by ancient DNA
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Hybridization as an invasion of the genome
inferredcites →https://doi.org/10.1016/j.tree.2009.01.009openalex-snapshot
Gene tree discordance, phylogenetic inference and the multispecies coalescent
inferredcites →https://doi.org/10.1073/pnas.1407950111openalex-snapshot
Maximum likelihood inference of reticulate evolutionary histories
inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot
Inferring Phylogeny Despite Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1089/cmb.2010.0102openalex-snapshot
Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences
inferredcites →https://doi.org/10.1093/bib/bby062openalex-snapshot
A review of metrics measuring dissimilarity for rooted phylogenetic networks
inferredcites →https://doi.org/10.1093/bioinformatics/18.2.337openalex-snapshot
Generating samples under a Wright–Fisher neutral model of genetic variation
inferredcites →https://doi.org/10.1093/bioinformatics/bty295openalex-snapshot
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/btz359openalex-snapshot
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data
inferredcites →https://doi.org/10.1093/genetics/155.2.945openalex-snapshot
Inference of Population Structure Using Multilocus Genotype Data
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040126openalex-snapshot
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
inferredcites →https://doi.org/10.1093/sysbio/syt012openalex-snapshot
Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syt037openalex-snapshot
Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syt059openalex-snapshot
Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syv118openalex-snapshot
Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods
inferredcites →https://doi.org/10.1093/sysbio/syw030openalex-snapshot
Inconsistency of Species Tree Methods under Gene Flow
inferredcites →https://doi.org/10.1093/sysbio/syw097openalex-snapshot
Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent
inferredcites →https://doi.org/10.1093/sysbio/syx044openalex-snapshot
Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events
inferredcites →https://doi.org/10.1093/sysbio/syx085openalex-snapshot
Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data
inferredcites →https://doi.org/10.1093/sysbio/syy015openalex-snapshot
Inferring Phylogenetic Networks Using PhyloNet
inferredcites →https://doi.org/10.1101/693986openalex-snapshot
Empirical Performance of Tree-based Inference of Phylogenetic Networks
inferredcites →https://doi.org/10.1109/tcbb.2009.2openalex-snapshot
A Metric on the Space of Reduced Phylogenetic Networks
inferredcites →https://doi.org/10.1109/tcbb.2009.33openalex-snapshot
On Nakhleh's Metric for Reduced Phylogenetic Networks
inferredcites →https://doi.org/10.1109/tcbb.2010.122openalex-snapshot
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
inferredcites →https://doi.org/10.1111/2041-210x.12694openalex-snapshot
A permutation approach for inferring species networks from gene trees in polyploid complexes by minimising deep coalescences
inferredcites →https://doi.org/10.1111/j.1471-8286.2005.01155.xopenalex-snapshot
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110316-022729openalex-snapshot
Phylogenetics of Allopolyploids
inferredcites →https://doi.org/10.1155/2014/254279openalex-snapshot
The Comparison of Tree-Sibling Time Consistent Phylogenetic Networks Is Graph Isomorphism-Complete
inferredcites →https://doi.org/10.1186/1471-2105-14-s15-s6openalex-snapshot
Fast algorithms and heuristics for phylogenomics under ILS and hybridization
inferredcites →https://doi.org/10.1186/1471-2105-14-s7-s6openalex-snapshot
GAM-NGS: genomic assemblies merger for next generation sequencing
inferredcites →https://doi.org/10.1186/1471-2105-9-322openalex-snapshot
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
inferredcites →https://doi.org/10.1186/1471-2148-9-216openalex-snapshot
Inferring polyploid phylogenies from multiply-labeled gene trees
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s10openalex-snapshot
A maximum pseudo-likelihood approach for phylogenetic networks
inferredcites →https://doi.org/10.1186/1745-6150-6-41openalex-snapshot
The public goods hypothesis for the evolution of life on Earth
inferredcites →https://doi.org/10.1186/s12859-016-1269-1openalex-snapshot
In the light of deep coalescence: revisiting trees within networks
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1186/s12864-020-6608-yopenalex-snapshot
Integrated likelihood for phylogenomics under a no-common-mechanism model
inferredcites →https://doi.org/10.1371/journal.pcbi.1000501openalex-snapshot
Species Tree Inference by Minimizing Deep Coalescences
inferredcites →https://doi.org/10.1371/journal.pcbi.1004135openalex-snapshot
Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
inferredcites →https://doi.org/10.1371/journal.pcbi.1005932openalex-snapshot
Bayesian inference of phylogenetic networks from bi-allelic genetic markers
inferredcites →https://doi.org/10.1371/journal.pcbi.1006177openalex-snapshot
A quantitative physical model of the TMS-induced discharge artifacts in EEG
inferredcites →https://doi.org/10.1371/journal.pgen.1002660openalex-snapshot
The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection
inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1006006openalex-snapshot
Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
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Identifiability of local and global features of phylogenetic networks from average distances
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Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider
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A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders
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Global phylogeny and taxonomy of Artemisia
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Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species
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Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region
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NetRAX: accurate and fast maximum likelihood phylogenetic network inference
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Insights from the genomes of 4 diploid Camelina spp.
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Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability
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A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth’s Largest Lizards
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Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs ( Occidozyga laevis )
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Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
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Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa
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Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes
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Origin and Diversification of the Saguaro Cactus (Carnegiea gigantea): A Within-Species Phylogenomic Analysis
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Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information
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Insights from the genomes of four diploid Camelina spp.
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Unraveling Phylogenetic Relationships, Reticulate Evolution, and Genome Composition of Polyploid Plant Complexes by Rad-Seq and Hyb-Seq
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Supporting per-locus substitution rates improves the accuracy of species networks and avoids spurious reticulations
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Genomic Insights into Derived Dwarfism and Exudivory in a Genus ( Callithrix ) of the World’s Smallest Anthropoid Monkeys
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Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora.
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Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto‐nuclear discordance and provides new insights into generic relationships
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Ancient hybridization patterns between bighorn and thinhorn sheep
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Prezygotic barriers effectively limit hybridization in a rapid evolutionary radiation
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The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization
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AllCoPol: inferring allele co-ancestry in polyploids
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Elucidation of the phylogeny of Cucurbitaceae, particularly Trichosanthes, based on plastome data and nuclear single-copy genes
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Natural Hybrid Origin of the Controversial “Species” Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence
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HP2NET: Empowering Efficient Phylogenetic Network Analysis through High-Performance Computing
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