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Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

https://doi.org/10.1371/journal.pgen.1005896

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/tax.562013openalex-snapshot

Concordance trees, concordance factors, and the exploration of reticulate genealogy

inferredcites →https://doi.org/10.1007/978-3-319-19048-8_32openalex-snapshot

A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1007/978-3-319-21233-3_10openalex-snapshot

Likelihood-Based Inference of Phylogenetic Networks from Sequence Data by PhyloDAG

inferredcites →https://doi.org/10.1007/s00285-010-0355-7openalex-snapshot

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

inferredcites →https://doi.org/10.1007/s00285-015-0899-7openalex-snapshot

Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations

inferredcites →https://doi.org/10.1007/s00440-006-0011-8openalex-snapshot

Minimal Penalties for Gaussian Model Selection

inferredcites →https://doi.org/10.1007/s11222-011-9236-1openalex-snapshot

Slope heuristics: overview and implementation

inferredcites →https://doi.org/10.1016/j.tpb.2008.10.004openalex-snapshot

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

inferredcites →https://doi.org/10.1016/j.ympev.2011.06.021openalex-snapshot

Quartet MaxCut: A fast algorithm for amalgamating quartet trees

inferredcites →https://doi.org/10.1017/cbo9780511974076openalex-snapshot

Phylogenetic Networks

inferredcites →https://doi.org/10.1073/pnas.1407950111openalex-snapshot

Maximum likelihood inference of reticulate evolutionary histories

inferredcites →https://doi.org/10.1073/pnas.1412627111openalex-snapshot

Speciation with gene flow in equids despite extensive chromosomal plasticity

inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

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/btg180openalex-snapshot

MrBayes 3: Bayesian phylogenetic inference under mixed models

inferredcites →https://doi.org/10.1093/bioinformatics/btq539openalex-snapshot

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot

ASTRAL: genome-scale coalescent-based species tree estimation

inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot

Quartet Inference from SNP Data Under the Coalescent Model

inferredcites →https://doi.org/10.1093/molbev/msl170openalex-snapshot

Bayesian Estimation of Concordance among Gene Trees

inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot

Testing for Ancient Admixture between Closely Related Populations

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026367openalex-snapshot

Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models

inferredcites →https://doi.org/10.1093/sysbio/syp055openalex-snapshot

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

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/syu087openalex-snapshot

Weighted Quartets Phylogenetics

inferredcites →https://doi.org/10.1093/sysbio/syv037openalex-snapshot

Which Phylogenetic Networks are Merely Trees with Additional Arcs?

inferredcites →https://doi.org/10.1093/sysbio/syw030openalex-snapshot

Inconsistency of Species Tree Methods under Gene Flow

inferredcites →https://doi.org/10.1109/tcbb.2008.52openalex-snapshot

The Identifiability of Covarion Models in Phylogenetics

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.2013.8openalex-snapshot

SuperQ: Computing Supernetworks from Quartets

inferredcites →https://doi.org/10.1126/science.1258524openalex-snapshot

Extensive introgression in a malaria vector species complex revealed by phylogenomics

inferredcites →https://doi.org/10.1126/science.aaa3600openalex-snapshot

Conundrum of jumbled mosquito genomes

inferredcites →https://doi.org/10.1142/s0219720012500047openalex-snapshot

QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS

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/10.1186/1471-2148-10-302openalex-snapshot

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s10openalex-snapshot

A maximum pseudo-likelihood approach for phylogenetic networks

inferredcites →https://doi.org/10.1186/1752-0509-8-21openalex-snapshot

Quartet-based methods to reconstruct phylogenetic networks

inferredcites →https://doi.org/10.1239/aap/1208358894openalex-snapshot

Identifiability of a Markovian model of molecular evolution with gamma-distributed rates

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.1005071openalex-snapshot

Inference of Ancestral Recombination Graphs through Topological Data Analysis

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/10.4230/lipics.ecoop.2017.4openalex-snapshot

Julia: A Fast Dynamic Language for Technical Computing

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Phylogenetics in space: How continuous spatial structure impacts tree inference

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107543openalex-snapshot

Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107581openalex-snapshot

Out of chaos: Phylogenomics of Asian Sonerileae

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107589openalex-snapshot

Phylogenetic assessment of the Metamasius hemipterus species complex (Coleoptera, Curculionidae, Dryophthorinae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107682openalex-snapshot

Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107727openalex-snapshot

Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107774openalex-snapshot

Multiple introgression events during the diversification history of the edible Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107808openalex-snapshot

Target sequence capture data shed light on the deeper evolutionary relationship on the subgenus Chamaecerasus of Lonicera (Caprifoliaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107837openalex-snapshot

Phylogenomic analyses of the Neotropical Artocarpeae (Moraceae) reveal a history of introgression and support the reinstatement of Acanthinophyllum

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107866openalex-snapshot

Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107892openalex-snapshot

Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107912openalex-snapshot

Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107914openalex-snapshot

Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107962openalex-snapshot

Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region

inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107965openalex-snapshot

Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108047openalex-snapshot

Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108066openalex-snapshot

Applications of Machine Learning in Phylogenetics

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108093openalex-snapshot

Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108112openalex-snapshot

Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108136openalex-snapshot

Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108159openalex-snapshot

Evolutionary relationships and fine-scale geographic structuring in the temperate percichthyid genus Gadopsis (blackfishes) to support fisheries and conservation management

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108160openalex-snapshot

Disentangling sources of gene tree discordance for Hordeum species via target-enriched sequencing assays

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108162openalex-snapshot

Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108197openalex-snapshot

Reticulate evolution: Detection and utility in the phylogenomics era

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108236openalex-snapshot

Nuclear phylogenomics of Eperua (Leguminosae) highlights the role of habitat and morphological lability in dispersal and diversification across Amazonia and in the Caatinga-Cerrado ecotone

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108288openalex-snapshot

Phylogenomics and species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq and morphological data

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108326openalex-snapshot

Phylogeny, species delimitation, and biogeographical history of Bredia

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108405openalex-snapshot

Phylogenomics reveals taxonomic challenges in Calibrachoa (Solanaceae) and sheds light on the origins of cultivated million bells

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108410openalex-snapshot

Population-Level Phylogenomic Analysis Yields Insights into Species Cohesion and Population Substructure of Lobelia Section Lobelia (Campanulaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108421openalex-snapshot

Integrated morphological and phylogenomic analyses revealed a novel genus Paramicrotoena (Lamiaceae − Pogostemoneae) discovered in the Pan-Himalaya

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108422openalex-snapshot

Phylogenomic insights into incomplete lineage sorting and hybridization in early-diverging eudicots

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108437openalex-snapshot

Reticulate evolution in terrestrial snails of Euhadra peliomphala species complex

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108444openalex-snapshot

Phylogenomic incongruence in Castanopsis (Fagaceae) is primarily caused by gene flow rather than incomplete lineage sorting

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108446openalex-snapshot

Geographic isolation, ecological adaptation, and hybridization influenced fast divergence of a Solanaceae plant group from subtropical highland grasslands

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108472openalex-snapshot

Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108517openalex-snapshot

Diversification and hybridization in Andinocleome (Cleomaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108525openalex-snapshot

Phylogenomics disentangles the evolutionary and biogeographic uncertainty in Apocissus (Vitaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108531openalex-snapshot

UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard genus Barisia (Squamata: Anguidae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108579openalex-snapshot

Phylogenomics of the woodland salamanders (Plethodon): Reticulate evolution and indistinct species boundaries

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108643openalex-snapshot

Eocene colonization of the Neotropics and Miocene expansion to South America explain the evolution of the amphi-Pacific disjunct genus Dendropanax (Araliaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108648openalex-snapshot

Deciphering reticulation and reproductive trait evolution in a chasmophyte lineage: a phylogenomic approach to the evolutionary patterns within Petrocoptis

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108652openalex-snapshot

Integrative taxonomic revision of Uropsilus (Uropsilinae, Talpidae) combining genomic, morphological and geographic evidence

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108663openalex-snapshot

Phylogenomic analyses of the Austral podocarps (Podocarpus: Podocarpaceae) support hybrid ancestry of a New Zealand species

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108664openalex-snapshot

Whole genome sequencing reveals the phylogenetic relationships and reticulate evolution of Phrynocephalus lizards in Eurasia

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108687openalex-snapshot

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108702openalex-snapshot

Introgression shapes the genomic conflict landscape of Malus, providing evidence for a reticulate backbone in a woody crop lineage

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108716openalex-snapshot

Complex evolutionary history of Rosales mediated by extensive incomplete lineage sorting and hybridization

inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108735openalex-snapshot

Phylogenomics and evolution of the Lauraceae based on targeted capture data

inferred← citeshttps://doi.org/10.1038/s41437-024-00683-4openalex-snapshot

A historical stepping-stone path for an island-colonizing cactus across a submerged “bridge” archipelago

inferred← citeshttps://doi.org/10.1038/s41467-022-28917-1openalex-snapshot

Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

inferred← citeshttps://doi.org/10.1038/s41467-022-33319-4openalex-snapshot

Early stages of sympatric homoploid hybrid speciation in crater lake cichlid fishes

inferred← citeshttps://doi.org/10.1038/s41467-024-50852-6openalex-snapshot

Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

inferred← citeshttps://doi.org/10.1038/s41467-025-62644-7openalex-snapshot

Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family

inferred← citeshttps://doi.org/10.1038/s41467-026-71057-zopenalex-snapshot

Scaling up Bayesian population phylogenomics through virtual dimension reduction

inferred← citeshttps://doi.org/10.1038/s41477-023-01562-2openalex-snapshot

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

inferred← citeshttps://doi.org/10.1038/s41576-026-00995-7openalex-snapshot

Genetics and genomics of hybridization

inferred← citeshttps://doi.org/10.1038/s41598-020-58279-xopenalex-snapshot

Genome-scale data reveal the role of hybridization in lichen-forming fungi

inferred← citeshttps://doi.org/10.1038/s41598-020-62446-5openalex-snapshot

A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes

inferred← citeshttps://doi.org/10.1038/s41598-024-60215-2openalex-snapshot

Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family

inferred← citeshttps://doi.org/10.1071/sb24011openalex-snapshot

Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data

inferred← citeshttps://doi.org/10.1073/pnas.2214076120openalex-snapshot

A global phylogenomic analysis of the shiitake genus Lentinula

inferred← citeshttps://doi.org/10.1073/pnas.2310708120openalex-snapshot

Efficient Bayesian inference under the multispecies coalescent with migration

inferred← citeshttps://doi.org/10.1073/pnas.2410934122openalex-snapshot

Phylogenetic networks empower biodiversity research

inferred← citeshttps://doi.org/10.1073/pnas.2421004122openalex-snapshot

Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation

inferred← citeshttps://doi.org/10.1073/pnas.2536533123openalex-snapshot

Reticulated adaptive radiation and phylogenomic diversity loss in the Hawaiian honeycreepers

inferred← citeshttps://doi.org/10.1080/11263504.2023.2287530openalex-snapshot

Disentangling the distribution of Adenostyles in the Northern Iberian Peninsula: new insights from nuclear and plastid markers

inferred← citeshttps://doi.org/10.1080/14772019.2022.2070717openalex-snapshot

The fossil record of sabre-tooth characins (Teleostei: Characiformes: Cynodontinae), their phylogenetic relationships and palaeobiogeographical implications

inferred← citeshttps://doi.org/10.1086/715056openalex-snapshot

A New Diploid Parthenogenetic Whiptail Lizard from Sonora, Mexico, Is the “Missing Link” in the Evolutionary Transition to Polyploidy

inferred← citeshttps://doi.org/10.1086/715636openalex-snapshot

Discordance in a South African Memecylon Clade (Melastomataceae): Evidence for Reticulate Evolution

inferred← citeshttps://doi.org/10.1089/cmb.2018.0129openalex-snapshot

A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality

inferred← citeshttps://doi.org/10.1089/cmb.2024.0710openalex-snapshot

Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs

inferred← citeshttps://doi.org/10.1093/aob/mcab139openalex-snapshot

Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization

inferred← citeshttps://doi.org/10.1093/aob/mcad008openalex-snapshot

Evolution of hygrophytic plant species in the Anatolia–Caucasus region: insights from phylogenomic analyses ofCardamineperennials

inferred← citeshttps://doi.org/10.1093/aob/mcae030openalex-snapshot

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae)

inferred← citeshttps://doi.org/10.1093/aob/mcae066openalex-snapshot

Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae)

inferred← citeshttps://doi.org/10.1093/aob/mcae073openalex-snapshot

Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: an example using California sages (Salvia subgenus Audibertia: Lamiaceae)

inferred← citeshttps://doi.org/10.1093/aob/mcae100openalex-snapshot

Phylogenetics and biogeography of the olive family (Oleaceae)

inferred← citeshttps://doi.org/10.1093/aob/mcae205openalex-snapshot

Climatic and edaphic niche shifts during plant radiation in the Mediterranean biodiversity hotspot

inferred← citeshttps://doi.org/10.1093/aob/mcae224openalex-snapshot

Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae)

inferred← citeshttps://doi.org/10.1093/aob/mcaf002openalex-snapshot

Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification

inferred← citeshttps://doi.org/10.1093/aob/mcaf212openalex-snapshot

Phylogenetics and evolution of Digitaria grasses, including cereal crops fonio, raishan and Polish millet

inferred← citeshttps://doi.org/10.1093/aob/mcaf329openalex-snapshot

Genomic insights into the rapid diversification of Petunia in a biodiversity hotspot in the South American grasslands

inferred← citeshttps://doi.org/10.1093/aob/mcag189openalex-snapshot

Phylogenomic conflict and reticulate evolution during radiative diversification of the genus Rheum

inferred← citeshttps://doi.org/10.1093/bioadv/vbae014openalex-snapshot

Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa863openalex-snapshot

Assessing the fit of the multi-species network coalescent to multi-locus data

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa868openalex-snapshot

MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac075openalex-snapshot

RF-Net 2: fast inference of virus reassortment and hybridization networks

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac396openalex-snapshot

NetRAX: accurate and fast maximum likelihood phylogenetic network inference

inferred← citeshttps://doi.org/10.1093/bioinformatics/btag245openalex-snapshot

CAMUS: scalable phylogenetic network estimation

inferred← citeshttps://doi.org/10.1093/bioinformatics/btag289openalex-snapshot

SNaQ.jl: Improved scalability for level-1 phylogenetic network inference

inferred← citeshttps://doi.org/10.1093/bioinformatics/bty295openalex-snapshot

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz476openalex-snapshot

Mycorrhiza: genotype assignment using phylogenetic networks

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