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

Canonical link: https://scholar.rpkg.net/pkg/phytools

Liam J. Revell • View description and downloads View dependencies GitHub project

2011 Published

2.1-1 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
Rtapas: Random Tanglegram Partitions (Version 1.1)	2022
treeplyr: "dplyr" Functionality for Matched Tree and Data Objects (Version 0.1.10)	2016
BAT: Biodiversity Assessment Tools (Version 2.9.6)	2014
Claddis: Measuring Morphological Diversity and Evolutionary Tempo (Version 0.6.3)	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)	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 3.5.0)	2021
RNeXML: Semantically Rich I/O for the 'NeXML' Format (Version 2.4.11)	2014
RPANDA: Phylogenetic ANalyses of DiversificAtion (Version 2.3)	2014
RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies (Version 2.8.0)	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
TML: Tropical Geometry Tools for Machine Learning (Version 1.2.0)	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 1.0.0)	2024
bite: Bayesian Integrative Models of Trait Evolution (Version 0.3)	2020
convevol: Analysis of Convergent Evolution (Version 2.0.1)	2013
corHMM: Hidden Markov Models of Character Evolution (Version 2.8)	2013
ctpm: Continuous-Time Phylogenetic Modeling (Version 1.0.1)	2021
datelife: Scientific Data on Time of Lineage Divergence for Your Taxa (Version 0.6.8)	2022
deeptime: Plotting Tools for Anyone Working in Deep Time (Version 1.1.1)	2021
evobiR: Comparative and Population Genetic Analyses (Version 1.1)	2013
fishtree: Interface to the Fish Tree of Life API (Version 0.3.4)	2018
funspace: Creating and Representing Functional Trait Spaces (Version 0.2.1)	2023
geiger: Analysis of Evolutionary Diversification (Version 2.0.11)	2007
hisse: Hidden State Speciation and Extinction (Version 2.1.11)	2015
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 1.1.9)	2014
nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty (Version 0.1.20)	2020
ontophylo: Ontology-Informed Phylogenetic Comparative Analyses (Version 1.1.3)	2023
palaeoverse: Prepare and Explore Data for Palaeobiological Analyses (Version 1.3.0)	2022
paleotree: Paleontological and Phylogenetic Analyses of Evolution (Version 3.4.5)	2012
pez: Phylogenetics for the Environmental Sciences (Version 1.2-4)	2014
phylosem: Phylogenetic Structural Equation Model (Version 1.1.4)	2023
pmc: Phylogenetic Monte Carlo (Version 1.0.6)	2012
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 1.3.0)	2018
secsse: Several Examined and Concealed States-Dependent Speciation and Extinction (Version 3.0.2)	2019
sensiPhy: Sensitivity Analysis for Comparative Methods (Version 0.8.5)	2016
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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