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Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees

https://doi.org/10.1093/bioinformatics/btaa614
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What this work says

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

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A Mathematical Theory of Communication
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A Mathematical Theory of Communication
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Computing and Combinatorics
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Some notes on the nearest neighbour interchange distance
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A Metric for Phylogenetic Trees Based on Matching
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Algorithms in Bioinformatics
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The Generalized Robinson-Foulds Metric
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The Information Content of Consensus Trees
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Obtaining common pruned trees
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Comparison of phylogenetic trees
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Reconstructing evolution of sequences subject to recombination using parsimony
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Comparing clusterings—an information based distance
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
inferredcites →https://doi.org/10.1093/acprof:oso/9780199297306.001.0001openalex-snapshot
Parsimony, Phylogeny, and Genomics
inferredcites →https://doi.org/10.1093/acprof:oso/9780199297306.003.0009openalex-snapshot
Maximum parsimony and the phylogenetic information in multistate characters
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Statistically based postprocessing of phylogenetic analysis by clustering
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A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot
phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/btu157openalex-snapshot
tqDist: a library for computing the quartet and triplet distances between binary or general trees
inferredcites →https://doi.org/10.1093/biolinnean/blab046openalex-snapshot
Information content of trees: three-taxon statements, inference rules and dependency
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/34.1.75openalex-snapshot
The Use of Tree Comparison Metrics
inferredcites →https://doi.org/10.1093/sysbio/42.2.126openalex-snapshot
Distributions of Tree Comparison Metrics--Some New Results
inferredcites →https://doi.org/10.1093/sysbio/syu085openalex-snapshot
Practical Performance of Tree Comparison Metrics
inferredcites →https://doi.org/10.1098/rsbl.2018.0632openalex-snapshot
Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets
inferredcites →https://doi.org/10.1109/tcbb.2011.157openalex-snapshot
A Metric for Phylogenetic Trees Based on Matching
inferredcites →https://doi.org/10.1109/tcbb.2011.48openalex-snapshot
Matching Split Distance for Unrooted Binary Phylogenetic Trees
inferredcites →https://doi.org/10.1109/tcbb.2018.2802911openalex-snapshot
Calculating the Unrooted Subtree Prune-and-Regraft Distance
inferredcites →https://doi.org/10.1111/cla.12160openalex-snapshot
TNT version 1.5, including a full implementation of phylogenetic morphometrics
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ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH
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The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
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Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima
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Compatibility Methods in Systematics
inferredcites →https://doi.org/10.1371/journal.pone.0020109openalex-snapshot
On the Accuracy of Language Trees
inferredcites →https://doi.org/10.2307/2412378openalex-snapshot
On Comparing the Shapes of Taxonomic Trees
inferredcites →https://doi.org/10.2307/2413326openalex-snapshot
Comparison of Undirected Phylogenetic Trees Based on Subtrees of Four Evolutionary Units
inferredcites →https://doi.org/10.2307/2413347openalex-snapshot
The Use of Tree Comparison Metrics
inferredcites →https://doi.org/10.2307/sysbio/34.2.193openalex-snapshot
Comparison of Undirected Phylogenetic Trees Based on Subtrees of Four Evolutionary Units
inferredcites →https://doi.org/10.2478/amcs-2013-0050openalex-snapshot
On a matching distance between rooted phylogenetic trees
inferredcites →https://doi.org/10.32614/cran.package.tbrdistopenalex-snapshot
TBRDist: Rearrangement Distances Between Phylogenetic Trees
inferredcites →https://doi.org/10.5281/zenodo.2536318openalex-snapshot
Quartet: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures
inferredcites →https://doi.org/10.5281/zenodo.3528123openalex-snapshot
TreeDist: Distances Between Phylogenetic Trees
inferredcites →https://doi.org/10.5555/1756006.1953024openalex-snapshot
Information Theoretic Measures for Clusterings Comparison: Variants, Properties, Normalization and Correction for Chance

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Bayesian Least-Squares Supertrees (BLeSS): Flexible Inference of Large Time-Calibrated Phylogenies
inferred← citeshttps://doi.org/10.1101/2024.12.12.628057openalex-snapshot
Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation
inferred← citeshttps://doi.org/10.1101/2025.01.08.631854openalex-snapshot
Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings
inferred← citeshttps://doi.org/10.1101/2025.04.22.650124openalex-snapshot
State Space Misspecification in Morphological Phylogenetics: A Pitfall for Models and Parsimony Alike
inferred← citeshttps://doi.org/10.1101/2025.11.28.691233openalex-snapshot
Admixture in a butterfly species complex creates a genomic mosaic of ancestry with distinct histories for different chromosomes
inferred← citeshttps://doi.org/10.1101/gr.279449.124openalex-snapshot
Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis
inferred← citeshttps://doi.org/10.1109/tsg.2023.3239650openalex-snapshot
An Improved Algorithm for Topology Identification of Distribution Networks Using Smart Meter Data and Its Application for Fault Detection
inferred← citeshttps://doi.org/10.1111/1755-0998.70163openalex-snapshot
Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria
inferred← citeshttps://doi.org/10.1111/2041-210x.14210openalex-snapshot
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits
inferred← citeshttps://doi.org/10.1111/cla.12540openalex-snapshot
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses
inferred← citeshttps://doi.org/10.1111/cla.12564openalex-snapshot
Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters
inferred← citeshttps://doi.org/10.1111/cla.12581openalex-snapshot
Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
inferred← citeshttps://doi.org/10.1111/cla.12606openalex-snapshot
Accuracy of phylogenetic reconstructions from continuous characters analysed under parsimony and its parametric correlates
inferred← citeshttps://doi.org/10.1111/cla.12614openalex-snapshot
On the effect of measures for comparing trees on the representation of treespace
inferred← citeshttps://doi.org/10.1111/cla.70054openalex-snapshot
Phylogenetic and ecological duality in the otoliths of Sciaenidae
inferred← citeshttps://doi.org/10.1111/ele.14490openalex-snapshot
Phylogeny structures species' interactions in experimental ecological communities
inferred← citeshttps://doi.org/10.1111/mec.17610openalex-snapshot
Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes
inferred← citeshttps://doi.org/10.1111/mec.70391openalex-snapshot
A Whole‐Genome Investigation of Mitonuclear Discordance in the Trematode Parasite Atriophallophorus winterbourni
inferred← citeshttps://doi.org/10.1111/nph.20263openalex-snapshot
A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence
inferred← citeshttps://doi.org/10.1111/pala.70031openalex-snapshot
Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data
inferred← citeshttps://doi.org/10.1111/syen.12686openalex-snapshot
Extensive hybridisation and complex evolutionary history in the leafhopper genus Agnesiella (Hemiptera: Cicadellidae: Typhlocybinae)
inferred← citeshttps://doi.org/10.1111/syen.70041openalex-snapshot
Phylogenomics illuminates the complex evolutionary history of Bibionomorpha (Diptera)
inferred← citeshttps://doi.org/10.1126/science.add9791openalex-snapshot
Erosion of heterogeneous rock drives diversification of Appalachian fishes
inferred← citeshttps://doi.org/10.1128/aem.00922-22openalex-snapshot
Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics
inferred← citeshttps://doi.org/10.1128/aem.01003-24openalex-snapshot
Microbiome divergence of marine gastropod species separated by the Isthmus of Panama
inferred← citeshttps://doi.org/10.1128/aem.01475-21openalex-snapshot
Genotyping and Multivariate Regression Trees Reveal Ecological Diversification within the Microcystis aeruginosa Complex along a Wide Environmental Gradient
inferred← citeshttps://doi.org/10.1128/jvi.01518-24openalex-snapshot
Host origin is a determinant of coevolution between gene segments of avian H9 influenza viruses
inferred← citeshttps://doi.org/10.1128/spectrum.03123-23openalex-snapshot
Phylogenomic analysis of the understudied Neisseriaceae species reveals a poly- and paraphyletic Kingella genus
inferred← citeshttps://doi.org/10.1144/jgs2021-111openalex-snapshot
Discussion on ‘ Tabelliscolex (Cricocosmiidae: Palaeoscolecidomorpha) from the early Cambrian Chengjiang Biota and the evolution of seriation in Ecdysozoa’ by Shi et al. 2021 ( JGS , jgs2021-060)
inferred← citeshttps://doi.org/10.1177/15578666251415567openalex-snapshot
Beyond Synteny: A Scalable Phylogenomics Method for Whole-Genome Duplication Detection
inferred← citeshttps://doi.org/10.1186/s12859-024-05997-yopenalex-snapshot
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space
inferred← citeshttps://doi.org/10.1186/s12862-024-02313-3openalex-snapshot
Do morphometric data improve phylogenetic reconstruction? A systematic review and assessment
inferred← citeshttps://doi.org/10.1186/s12864-025-12340-zopenalex-snapshot
A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila
inferred← citeshttps://doi.org/10.1186/s12915-022-01284-5openalex-snapshot
Early cephalopod evolution clarified through Bayesian phylogenetic inference
inferred← citeshttps://doi.org/10.1186/s12915-025-02135-9openalex-snapshot
Phylogenomics of angiosperms based on mitochondrial genes: insights into deep node relationships
inferred← citeshttps://doi.org/10.1186/s12917-026-05504-wopenalex-snapshot
Beyond labels: current sequencing data do not support standardized porcine circovirus 3 (PCV3) genotypes
inferred← citeshttps://doi.org/10.1186/s13015-023-00232-4openalex-snapshot
phyBWT2: phylogeny reconstruction via eBWT positional clustering
inferred← citeshttps://doi.org/10.1186/s13059-022-02794-9openalex-snapshot
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
inferred← citeshttps://doi.org/10.1186/s13073-026-01599-wopenalex-snapshot
Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations
inferred← citeshttps://doi.org/10.1186/s40168-025-02206-7openalex-snapshot
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
inferred← citeshttps://doi.org/10.1206/0003-0090.473.1.1openalex-snapshot
Codex Eurypterida: A Revised Taxonomy Based on Concordant Parsimony and Bayesian Phylogenetic Analyses
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011871openalex-snapshot
Robust expansion of phylogeny for fast-growing genome sequence data
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1014370openalex-snapshot
Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings
inferred← citeshttps://doi.org/10.1371/journal.pone.0258693openalex-snapshot
Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy
inferred← citeshttps://doi.org/10.17169/refubium-44917openalex-snapshot
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
inferred← citeshttps://doi.org/10.2110/palo.2023.041openalex-snapshot
MORPHOTYPE MATTERS: AN EXPERIMENTAL ANALYSIS OF THE MORPHOLOGICAL FIDELITY OF GASTROPOD STEINKERNS
inferred← citeshttps://doi.org/10.24042/biosfer.v15i1.21064openalex-snapshot
An In Silico Approach for Evaluation of ITS, rbcL, and psbA-trnH for DNA Barcoding of Eugenia spp.
inferred← citeshttps://doi.org/10.24072/pcjournal.667openalex-snapshot
The effects of host phylogenetic coverage and congruence metric on Monte Carlo-based null models of phylosymbiosis
inferred← citeshttps://doi.org/10.25080/nvyf1037openalex-snapshot
Ecological and Spatial Influences on the Genetics of Cumacea (Crustacea: Peracarida) in the Northern North Atlantic
inferred← citeshttps://doi.org/10.32614/cran.package.constreeopenalex-snapshot
ConsTree: Fast Algorithms for Phylogenetic Consensus Trees
inferred← citeshttps://doi.org/10.32614/cran.package.quartetopenalex-snapshot
Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures
inferred← citeshttps://doi.org/10.32614/cran.package.rogueopenalex-snapshot
Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees
inferred← citeshttps://doi.org/10.32614/cran.package.treedistopenalex-snapshot
TreeDist: Calculate and Map Distances Between Phylogenetic Trees
inferred← citeshttps://doi.org/10.32614/cran.package.treesearchopenalex-snapshot
TreeSearch: Phylogenetic Analysis with Discrete Character Data
inferred← citeshttps://doi.org/10.32614/rj-2023-019openalex-snapshot
TreeSearch: Morphological Phylogenetic Analysis in R
inferred← citeshttps://doi.org/10.33612/diss.985985382openalex-snapshot
The Evolutionary History of Baleen Whales in The Genome Era
inferred← citeshttps://doi.org/10.3389/fmicb.2021.626759openalex-snapshot
Phylogenetic Revision of the Genus Aliivibrio: Intra- and Inter-Species Variance Among Clusters Suggest a Wider Diversity of Species
inferred← citeshttps://doi.org/10.3389/fmicb.2021.730045openalex-snapshot
The 5′ and 3′ Untranslated Regions of the Japanese Encephalitis Virus (JEV): Molecular Genetics and Higher Order Structures
inferred← citeshttps://doi.org/10.3389/fmicb.2022.897656openalex-snapshot
Phylogenomic analysis of the genus Leuconostoc
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1732254openalex-snapshot
Molecular epidemiology of HIV-1 in Hungary: an evolving contact zone of colliding virus subtypes
inferred← citeshttps://doi.org/10.3389/fmolb.2024.1432495openalex-snapshot
Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees
inferred← citeshttps://doi.org/10.3389/fpls.2021.767478openalex-snapshot
Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
inferred← citeshttps://doi.org/10.3389/fpls.2023.1237749openalex-snapshot
Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny
inferred← citeshttps://doi.org/10.3390/a17010015openalex-snapshot
Computing RF Tree Distance over Succinct Representations
inferred← citeshttps://doi.org/10.3390/cells10020362openalex-snapshot
Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution
inferred← citeshttps://doi.org/10.3390/d14040284openalex-snapshot
DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?
inferred← citeshttps://doi.org/10.3390/e24020141openalex-snapshot
Prediction of Time Series Gene Expression and Structural Analysis of Gene Regulatory Networks Using Recurrent Neural Networks
inferred← citeshttps://doi.org/10.3390/plants14101478openalex-snapshot
The Genus Petunia (Solanaceae): Evolutionary Synthesis and Taxonomic Review
inferred← citeshttps://doi.org/10.3390/sym16070790openalex-snapshot
Novel Algorithm for Comparing Phylogenetic Trees with Different but Overlapping Taxa
inferred← citeshttps://doi.org/10.3847/1538-4357/ad036aopenalex-snapshot
On the Evolutionary History of a Simulated Disk Galaxy as Seen by Phylogenetic Trees
inferred← citeshttps://doi.org/10.4049/jimmunol.2300851openalex-snapshot
Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser
inferred← citeshttps://doi.org/10.47749/t/unicamp.2022.1260903openalex-snapshot
Extensions and applications of the genomic rank distance
inferred← citeshttps://doi.org/10.48130/gcomm-0026-0015openalex-snapshot
eGPS-oneBuilder: an integrated GUI-CLI workflow for sequence-based phylogenetic tree construction, structure-informed clustering, and interactive tree interpretation
inferred← citeshttps://doi.org/10.5194/egusphere-2024-3383openalex-snapshot
Phylogeochemistry: exploring evolutionary constraints on belemnite rostrum element composition
inferred← citeshttps://doi.org/10.5194/egusphere-2024-3383-ac1openalex-snapshot
Reply on RC1
inferred← citeshttps://doi.org/10.5194/egusphere-2024-3383-ac2openalex-snapshot
Reply on RC2
inferred← citeshttps://doi.org/10.6084/m9.figshare.19602439openalex-snapshot
Additional file 1 of Early cephalopod evolution clarified through Bayesian phylogenetic inference
inferred← citeshttps://doi.org/10.6084/m9.figshare.26608350openalex-snapshot
Additional file 1 of phyBWT2: phylogeny reconstruction via eBWT positional clustering
inferred← citeshttps://doi.org/10.64898/2026.01.05.697767openalex-snapshot
Guide scaffolding improves phylogenetic accuracy and enables integration across 16S amplicon regions
inferred← citeshttps://doi.org/10.64898/2026.01.20.700630openalex-snapshot
FastSpeciesTree: Fast and Scalable Species tree Inference
inferred← citeshttps://doi.org/10.64898/2026.05.14.725274openalex-snapshot
Resolving the oak tree of life: comparing RADseq and whole genome resequencing methods for oak phylogenetics
inferred← citeshttps://doi.org/10.64898/2026.05.26.723419openalex-snapshot
Alignment-free phylogenetic inference via hyperbolic protein language models
inferred← citeshttps://doi.org/10.64898/2026.06.20.733495openalex-snapshot
Evidence for post-allopolyploidy genetic exchanges between duplicated regions in three ancient polyploidies
inferred← citeshttps://doi.org/10.7554/elife.66525openalex-snapshot
Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
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