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apTreeshape: statistical analysis of phylogenetic tree shape

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

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On the distribution of binary search trees under the random permutation model
inferredcites →https://doi.org/10.1016/j.mbs.2005.03.003openalex-snapshot
On statistical tests of phylogenetic tree imbalance: The Sackin and other indices revisited
inferredcites →https://doi.org/10.1038/35074179openalex-snapshot
Phylogeny and the origin of HIV-1
inferredcites →https://doi.org/10.1086/419657openalex-snapshot
Inferring Evolutionary Process from Phylogenetic Tree Shape
inferredcites →https://doi.org/10.1093/bioinformatics/btg188openalex-snapshot
Pandit: a database of protein and associated nucleotide domains with inferred trees
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/bti175openalex-snapshot
SYMMETREE: whole-tree analysis of differential diversification rates
inferredcites →https://doi.org/10.1093/oso/9780198509424.001.0001openalex-snapshot
Phylogenetics
inferredcites →https://doi.org/10.1098/rstb.1925.0002openalex-snapshot
II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S
inferredcites →https://doi.org/10.1111/j.1558-5646.1993.tb02144.xopenalex-snapshot
SEARCHING FOR EVOLUTIONARY PATTERNS IN THE SHAPE OF A PHYLOGENETIC TREE
inferredcites →https://doi.org/10.1126/science.273.5275.569openalex-snapshot
The Roots of Phylogeny
inferredcites →https://doi.org/10.1214/ss/998929474openalex-snapshot
Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today
inferredcites →https://doi.org/10.1554/0014-3820(2001)055[0661:isrfp]2.0.co;2openalex-snapshot
INFERRING SPECIATION RATES FROM PHYLOGENIES
inferredcites →https://doi.org/10.2307/2409983openalex-snapshot
Searching for Evolutionary Patterns in the Shape of a Phylogenetic Tree

What points at this work

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

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A subfunctionalisation model of gene family evolution predicts balanced tree shapes
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Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates
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The productivity-biodiversity relationship varies across diversity dimensions
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Radiation and Divergence Times of Batoidea
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Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia
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Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling
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Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data
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Evolutionary Sample Size and Consilience in Phylogenetic Comparative Analysis
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Accuracy in Near-Perfect Virus Phylogenies
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The Major Features of Macroevolution
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But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating
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The Trouble with Topology: Phylogenies without Fossils Provide a Revisionist Perspective of Evolutionary History in Topological Analyses of Diversity
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Anomalous Unrooted Gene Trees
inferred← citeshttps://doi.org/10.1093/sysbio/syt033openalex-snapshot
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets
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The Shape of Modern Tree Reconstruction Methods
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Competitive Release Leads to Range Expansion and Rampant Speciation in Malagasy Dung Beetles
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How Ecology and Landscape Dynamics Shape Phylogenetic Trees
inferred← citeshttps://doi.org/10.1093/sysbio/syw019openalex-snapshot
Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?
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A Metric on Phylogenetic Tree Shapes
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Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity
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Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity
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Signatures of Microevolutionary Processes in Phylogenetic Patterns
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The spatio-temporal colonization and diversification across the Indo-Pacific by a ‘great speciator’ (Aves,Erythropitta erythrogaster)
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Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library
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An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life
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Phylogenetics, divergence times and diversification from three genomic partitions in monocots
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Phylogenetic analyses of G ammaridae crustacean reveal different diversification patterns among sister lineages in the Tethyan region
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Diversity, extinction, and threat status in Lagomorphs
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Speciation History Shapes Patterns of Assemblage Species Richness in Birds
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Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru
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The origins and diversification of C4 grasses and savanna‐adapted ungulates
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NEUTRAL BIODIVERSITY THEORY CAN EXPLAIN THE IMBALANCE OF PHYLOGENETIC TREES BUT NOT THE TEMPO OF THEIR DIVERSIFICATION
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Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the A frican spotted reed frog
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The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates
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Phylogenetic sampling affects evolutionary patterns of morphological disparity
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Neotropical ant parasitoids (Hymenoptera: Eucharitidae): interpreting taxonomy, phylogeny and divergent morphologies
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Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex
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Comparing tree shapes: beyond symmetry
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On Sackin’s original proposal: the variance of the leaves’ depths as a phylogenetic balance index
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J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments
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Density-Dependent Cladogenesis in Birds
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Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages
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Inferring the Dynamics of Diversification: A Coalescent Approach
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Measuring Asymmetry in Time-Stamped Phylogenies
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Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection
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Inference of Transmission Network Structure from HIV Phylogenetic Trees
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Matrilineal Fertility Inheritance Detected in Hunter–Gatherer Populations Using the Imbalance of Gene Genealogies
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NSAIDs Modulate Clonal Evolution in Barrett's Esophagus
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Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws
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Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients
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Secondary Sympatry Caused by Range Expansion Informs on the Dynamics of Microendemism in a Biodiversity Hotspot
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Evolutionary Dynamics in the Southwest Indian Ocean Marine Biodiversity Hotspot: A Perspective from the Rocky Shore Gastropod Genus Nerita
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Phylogenetic Molecular Species Delimitations Unravel Potential New Species in the Pest Genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae)
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Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution
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The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation
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A new resolution function to evaluate tree shape statistics
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Network science inspires novel tree shape statistics
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Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
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Phylogenetic and phenotypic divergence of an insular radiation of birds
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Stochastic tree models and probabilistic modelling of gene trees of given species networks
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Metacommunity phylogenteic structure along environmental gradients
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Phylogenetic Comparative Methods: Learning From Trees
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Oil disturbance reduces infaunal family richness but does not affect phylogenetic diversity
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MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells
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PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources
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PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics
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Counting, grafting and evolving binary trees
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Inferring Multi-Type Birth-Death Parameters for a Structured Host Population with Application to HIV Epidemic in Africa
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Two results on expected values of imbalance indices of phylogenetic trees
inferred← citeshttps://doi.org/10.48550/arxiv.2109.12281openalex-snapshot
Tree balance indices: a comprehensive survey
inferred← citeshttps://doi.org/10.6084/m9.figshare.12186144openalex-snapshot
Additional file 1 of On Sackin’s original proposal: the variance of the leaves’ depths as a phylogenetic balance index
inferred← citeshttps://doi.org/10.70675/317d122fzc25dz4a20z9770z102788f4b6afopenalex-snapshot
The European wildcat as a model for the study of wildlife : focus on hybridization and the circulation of viruses
inferred← citeshttps://doi.org/10.70675/35114307zb5a9z4d3az969az6fc47b55e2d6openalex-snapshot
Phylogeny and evolution of a highly diversified catfish subfamily : the Loricariinae (Siluriformes, Loricariidae)
inferred← citeshttps://doi.org/10.70675/fca7e2e2z8001z41edzbeefz9de527322bd9openalex-snapshot
Structure fonctionnelle des assemblages ichtyologiques le long de gradients environnementaux (système lagunaire de Patos-Mirim, Brésil)
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FSA: A Fast Stepwise Addition Algorithm for Constructing Phylogenetic Trees
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