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Empirical Performance of Tree-based Inference of Phylogenetic Networks

https://doi.org/10.1101/693986
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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-030-10837-3_13openalex-snapshot
Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
inferredcites →https://doi.org/10.1007/978-3-642-13214-8_12openalex-snapshot
Two Results on Distances for Phylogenetic Networks
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1073/pnas.1407950111openalex-snapshot
Maximum likelihood inference of reticulate evolutionary histories
inferredcites →https://doi.org/10.1089/cmb.2012.0234openalex-snapshot
Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
inferredcites →https://doi.org/10.1089/cmb.2015.0228openalex-snapshot
On Tree-Based Phylogenetic Networks
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/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/molbev/msx307openalex-snapshot
Bayesian Inference of Species Networks from Multilocus Sequence Data
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/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/10.1093/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/10.1109/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/10.1186/1471-2105-14-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/10.1186/1471-2164-16-s10-s10openalex-snapshot
A maximum pseudo-likelihood approach for phylogenetic networks
inferredcites →https://doi.org/10.1186/1471-2164-16-s8-s1openalex-snapshot
Better prediction of functional effects for sequence variants
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/s12862-018-1130-4openalex-snapshot
Phylogenomics of a rapid radiation: the Australian rainbow skinks
inferredcites →https://doi.org/10.1371/journal.pcbi.1006220openalex-snapshot
Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology
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.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.

inferred← citeshttps://doi.org/10.1007/978-3-031-48959-4_3openalex-snapshot
Progress on Constructing Phylogenetic Networks for Languages
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab267openalex-snapshot
Advancing admixture graph estimation via maximum likelihood network orientation
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag245openalex-snapshot
CAMUS: scalable phylogenetic network estimation
inferred← citeshttps://doi.org/10.1093/sysbio/syab081openalex-snapshot
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes
inferred← citeshttps://doi.org/10.1093/sysbio/syaf039openalex-snapshot
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization
inferred← citeshttps://doi.org/10.1101/746362openalex-snapshot
Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
inferred← citeshttps://doi.org/10.1101/gr.282203.126openalex-snapshot
Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under the network multispecies coalescent
inferred← citeshttps://doi.org/10.1111/cla.12578openalex-snapshot
PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks
inferred← citeshttps://doi.org/10.18061/bssb.v2i3.9285openalex-snapshot
Exploring the Distribution of Phylogenetic Networks Generated Under a Birth-Death-Hybridization Process
inferred← citeshttps://doi.org/10.18061/bssb.v3i1.9553openalex-snapshot
The Impact of Model Misspecification on Phylogenetic Network Inference
inferred← citeshttps://doi.org/10.3389/fbinf.2025.1571568openalex-snapshot
Integrating phylogenies with chronology to assemble the tree of life
inferred← citeshttps://doi.org/10.3389/fpls.2024.1324358openalex-snapshot
Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae)
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