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UglyTrees: a browser-based multispecies coalescent tree visualizer

https://doi.org/10.1093/bioinformatics/btaa679

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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/s00285-016-1034-0openalex-snapshot

Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent

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/10.1016/j.ympev.2018.12.029openalex-snapshot

Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko

inferredcites →https://doi.org/10.1017/s0031182019000428openalex-snapshot

Evaluation of the multispecies coalescent method to explore intra-Trypanosoma cruzi I relationships and genetic diversity

inferredcites →https://doi.org/10.1080/10635150802044011openalex-snapshot

Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)

inferredcites →https://doi.org/10.1093/bioinformatics/btx155openalex-snapshot

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

inferredcites →https://doi.org/10.1093/bioinformatics/bty633openalex-snapshot

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot

Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot

Bayesian Inference of Species Trees from Multilocus Data

inferredcites →https://doi.org/10.1093/molbev/msx126openalex-snapshot

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

inferredcites →https://doi.org/10.1093/molbev/msy147openalex-snapshot

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot

Relationships between gene trees and species trees.

inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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/syw018openalex-snapshot

Gene Tree Discordance Causes Apparent Substitution Rate Variation

inferredcites →https://doi.org/10.1093/sysbio/syw021openalex-snapshot

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

inferredcites →https://doi.org/10.1093/sysbio/syy026openalex-snapshot

A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics

inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150500openalex-snapshot

Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales

inferredcites →https://doi.org/10.1186/1471-2105-8-460openalex-snapshot

Dendroscope: An interactive viewer for large phylogenetic trees

inferredcites →https://doi.org/10.1186/1471-2148-13-44openalex-snapshot

Simulating gene trees under the multispecies coalescent and time-dependent migration

What points at this work

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

inferred← citeshttps://doi.org/10.3897/phytokeys.265.165998zenodo-depositor-declared

Phylogenetic analysis suggests early divergence followed by convergent morphological evolution in the Silene sections Odontopetalae and Sordidae (Caryophyllaceae)

inferred← citeshttps://doi.org/10.1007/978-3-031-23101-8_7openalex-snapshot

Visualizing Multispecies Coalescent Trees: Drawing Gene Trees Inside Species Trees

inferred← citeshttps://doi.org/10.1007/978-3-031-49272-3_14openalex-snapshot

Tree Drawings with Columns

inferred← citeshttps://doi.org/10.1016/j.genrep.2025.102224openalex-snapshot

A reappraisal of chloroplast genetic SNPs in phylogeny and barcoding of Pteris species (genus Pteris L.): Multispecies coalescence analysis, ancient hybridization, and deep coalescence

inferred← citeshttps://doi.org/10.1016/j.isci.2026.117803openalex-snapshot

Diversification and hybridization within the Spirochona gemmipara complex driven by gammarid host range shifts

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107631openalex-snapshot

Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108070openalex-snapshot

Revision of the ‘Acanthephyra purpurea’ species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic

inferred← citeshttps://doi.org/10.1038/s41467-022-34186-9openalex-snapshot

Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border

inferred← citeshttps://doi.org/10.1038/s42003-022-03723-zopenalex-snapshot

Quantitatively defining species boundaries with more efficiency and more biological realism

inferred← citeshttps://doi.org/10.1093/nar/gkad1160openalex-snapshot

Enzymic recognition of amino acids drove the evolution of primordial genetic codes

inferred← citeshttps://doi.org/10.1093/sysbio/syac010openalex-snapshot

StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent

inferred← citeshttps://doi.org/10.1093/sysbio/syad043openalex-snapshot

The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex)

inferred← citeshttps://doi.org/10.1093/sysbio/syae048openalex-snapshot

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models

inferred← citeshttps://doi.org/10.1093/ve/veab028openalex-snapshot

Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene

inferred← citeshttps://doi.org/10.1101/2021.10.06.463424openalex-snapshot

StarBeast3: Adaptive Parallelised Bayesian Inference of the Multispecies Coalescent

inferred← citeshttps://doi.org/10.1111/1749-4877.70192openalex-snapshot

Uncoupled Histories in the Largest Continental Arc of North America: Goodeid Fishes and Their Gyrodactylid Parasites Influenced Differently by the Trans‐Mexican Volcanic Belt

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008322openalex-snapshot

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model

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