R Package Scholar
28,794

phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Liam J. Revell   View description and downloadsView dependenciesGitHub project

2011 Published
2.3-0 Version
0 Citations
1 Authors
Referenced by ⇅ Year
brranching: Fetch "Phylogenies" from Many Sources (Version 0.7.0)

2015
perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data (Version 0.2.1)

2019
pirouette: Create a Bayesian Posterior from a Phylogeny (Version 1.6.9)

2022
Rarefy: Rarefaction Methods (Version 1.1.1)

2020
treeplyr: "dplyr" Functionality for Matched Tree and Data Objects (Version 0.1.10)

2016
bite: Bayesian Integrative Models of Trait Evolution (Version 0.3)

2020
datelife: Scientific Data on Time of Lineage Divergence for Your Taxa (Version 0.6.8)

2022
nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty (Version 0.1.20)

2020
BAT: Biodiversity Assessment Tools (Version 2.9.6)

2014
Claddis: Measuring Morphological Diversity and Evolutionary Tempo (Version 0.7.0)

2015
DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction (Version 4.4.1)

2015
DDD: Diversity-Dependent Diversification (Version 5.2.2)

2012
FishPhyloMaker: Phylogenies for a List of Finned-Ray Fishes (Version 0.2.0)

2021
GIFT: Access to the Global Inventory of Floras and Traits (GIFT) (Version 1.3.2)

2023
MonoPhy: Explore Monophyly of Taxonomic Groups in a Phylogeny (Version 1.3.2)

2015
OUwie: Analysis of Evolutionary Rates in an OU Framework (Version 2.10)

2011
PBD: Protracted Birth-Death Model of Diversification (Version 1.4)

2014
PhySortR: A Fast, Flexible Tool for Sorting Phylogenetic Trees (Version 1.0.8)

2015
PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM (Version 1.7.0)

2017
Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.6.0)

2021
RNeXML: Semantically Rich I/O for the 'NeXML' Format (Version 2.4.11)

2014
RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies (Version 2.8.1)

2018
RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses (Version 1.2.1)

2021
Rphylopars: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation (Version 0.3.10)

2015
Rtapas: Random Tanglegram Partitions (Version 1.2)

2022
TML: Tropical Geometry Tools for Machine Learning (Version 2.3.0)

2023
adiv: Analysis of Diversity (Version 2.2.1)

2017
arakno: ARAchnid KNowledge Online (Version 1.3.0)

2021
avotrex: A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder (Version 1.3.0)

2024
convevol: Analysis of Convergent Evolution (Version 2.2.1)

2013
corHMM: Hidden Markov Models of Character Evolution (Version 2.8)

2013
ctpm: Continuous-Time Phylogenetic Modeling (Version 1.0.1)

2021
deeptime: Plotting Tools for Anyone Working in Deep Time (Version 2.1.0)

2021
do3PCA: Probabilistic Phylogenetic Principal Component Analysis (Version 1.0.0)

2024
evobiR: Comparative and Population Genetic Analyses (Version 1.1)

2013
evolved: Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries (Version 1.0.0)

2024
fishtree: Interface to the Fish Tree of Life API (Version 0.3.4)

2018
funspace: Creating and Representing Functional Trait Spaces (Version 0.2.2)

2023
geiger: Analysis of Evolutionary Diversification (Version 2.0.11)

2007
hisse: Hidden State Speciation and Extinction (Version 2.1.11)

2015
holobiont: Microbiome Analysis Tools (Version 0.1.2)

2024
idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices (Version 2.0.13)

2019
learnPopGen: Population Genetic Simulations & Numerical Analysis (Version 1.0.4)

2018
mvMORPH: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data (Version 1.2.1)

2013
ontophylo: Ontology-Informed Phylogenetic Comparative Analyses (Version 1.1.3)

2023
orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants (Version 0.1.6)

2024
palaeoverse: Prepare and Explore Data for Palaeobiological Analyses (Version 1.4.0)

2022
paleotree: Paleontological and Phylogenetic Analyses of Evolution (Version 3.4.7)

2012
pez: Phylogenetics for the Environmental Sciences (Version 1.2-4)

2014
phylopairs: Comparative Analyses of Lineage-Pair Traits (Version 0.1.0)

2024
phylosem: Phylogenetic Structural Equation Model (Version 1.1.4)

2023
pmc: Phylogenetic Monte Carlo (Version 1.0.6)

2012
poweRbal: Phylogenetic Tree Models and the Power of Tree Shape Statistics (Version 0.0.1.1)

2024
ppgm: PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions (Version 1.0.3)

2024
qlcData: Processing Data for Quantitative Language Comparison (Version 0.3)

2015
ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix (Version 1.2.4)

2018
recluster: Ordination Methods for the Analysis of Beta-Diversity Indices (Version 2.9)

2013
rhierbaps: Clustering Genetic Sequence Data Using the HierBAPS Algorithm (Version 1.1.4)

2018
rphylopic: Get Silhouettes of Organisms from PhyloPic (Version 1.5.0)

2018
secsse: Several Examined and Concealed States-Dependent Speciation and Extinction (Version 3.1.0)

2019
sensiPhy: Sensitivity Analysis for Comparative Methods (Version 0.8.5)

2016
surface: Fitting Hansen Models to Investigate Convergent Evolution (Version 0.6)

2013
tapnet: Trait Matching and Abundance for Predicting Bipartite Networks (Version 0.3)

2021
treestartr: Generate Starting Trees for Combined Molecular, Morphological and Stratigraphic Data (Version 0.1.0)

2019
treespace: Statistical Exploration of Landscapes of Phylogenetic Trees (Version 1.1.4.3)

2017
windex: Analysing Convergent Evolution using the Wheatsheaf Index (Version 2.0.8)

2014

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