phangorn: Phylogenetic Reconstruction and Analysis

Canonical link: https://rscholar.com/pkg/phangorn

Klaus Schliep • Emmanuel Paradis • Leonardo de Oliveira Martins • Alastair Potts • Iris Bardel-Kahr • Tim W. White • Cyrill Stachniss • Michelle Kendall • Keren Halabi • Richel Bilderbeek • Kristin Winchell • Liam Revell • Mike Gilchrist • Jeremy Beaulieu • Brian O'Meara • Long Qu • Joseph Brown • Santiago Claramunt • View description and downloads View dependencies GitHub project

2008 Published

2.12.1 Version

0 Citations

18 Authors

Referenced by ⇅	Year
liayson: Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes (Version 1.0.5)	2018
pirouette: Create a Bayesian Posterior from a Phylogeny (Version 1.6.9)	2022
prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies (Version 1.1.1)	2020
datelife: Scientific Data on Time of Lineage Divergence for Your Taxa (Version 0.6.8)	2022
taxize: Taxonomic Information from Around the Web (Version 0.9.100.1)	2012
BSS: Brownian Semistationary Processes (Version 0.1.0)	2020
BoSSA: A Bunch of Structure and Sequence Analysis (Version 3.7)	2009
CongreveLamsdell2016: Distance Metrics for Trees Generated by Congreve and Lamsdell (Version 1.0.3)	2019
DCLEAR: Distance Based Cell Lineage Reconstruction (Version 1.0.13)	2021
EnvNJ: Whole Genome Phylogenies Using Sequence Environments (Version 0.1.3)	2021
LDM: Testing Hypotheses About the Microbiome using the Linear Decomposition Model (Version 6.0.1)	2023
MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent (Version 3.0)	2019
MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis (Version 0.10.1)	2024
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
POMS: Phylogenetic Organization of Metagenomic Signals (Version 1.0.1)	2022
Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.6.0)	2021
Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures (Version 1.2.7)	2019
RPANDA: Phylogenetic ANalyses of DiversificAtion (Version 2.3)	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
STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny (Version 1.1.2)	2019
SeqFeatR: A Tool to Associate FASTA Sequences and Features (Version 0.3.1)	2014
TML: Tropical Geometry Tools for Machine Learning (Version 2.3.0)	2023
TreeDist: Calculate and Map Distances Between Phylogenetic Trees (Version 2.9.1)	2020
TreeSearch: Phylogenetic Analysis with Discrete Character Data (Version 1.5.1)	2017
TreeTools: Create, Modify and Analyse Phylogenetic Trees (Version 1.12.0)	2019
ape: Analyses of Phylogenetics and Evolution (Version 5.8)	2002
apex: Phylogenetic Methods for Multiple Gene Data (Version 1.0.6)	2015
babette: Control 'BEAST2' (Version 2.3.4)	2020
beastier: Call 'BEAST2' (Version 2.5.2)	2019
coalescentMCMC: MCMC Algorithms for the Coalescent (Version 0.4-4)	2012
corHMM: Hidden Markov Models of Character Evolution (Version 2.8)	2013
dendextend: Extending 'dendrogram' Functionality in R (Version 1.18.1)	2014
dispRity: Measuring Disparity (Version 1.8)	2018
dowser: B Cell Receptor Phylogenetics Toolkit (Version 2.3)	2021
genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data (Version 1.2.7)	2017
gromovlab: Gromov-Hausdorff Type Distances for Labeled Metric Spaces (Version 0.8-3)	2015
haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony (Version 1.1.3.1)	2015
hisse: Hidden State Speciation and Extinction (Version 2.1.11)	2015
immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires (Version 0.9.1)	2020
indelmiss: Insertion Deletion Analysis While Accounting for Possible Missing Data (Version 1.0.10)	2016
ips: Interfaces to Phylogenetic Software in R (Version 0.0.12)	2014
markophylo: Markov Chain Models for Phylogenetic Trees (Version 1.0.9)	2015
mcbette: Model Comparison Using 'babette' (Version 1.15.3)	2020
microbial: Do 16s Data Analysis and Generate Figures (Version 0.0.21)	2020
nodeSub: Simulate DNA Alignments Using Node Substitutions (Version 1.2.8)	2021
orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants (Version 0.1.5)	2024
paleotree: Paleontological and Phylogenetic Analyses of Evolution (Version 3.4.7)	2012
pcmabc: Approximate Bayesian Computations for Phylogenetic Comparative Methods (Version 1.1.3)	2018
phyloregion: Biogeographic Regionalization and Macroecology (Version 1.0.8)	2020
phytools: Phylogenetic Tools for Comparative Biology (and Other Things) (Version 2.3-0)	2011
ppgm: PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions (Version 1.0.3)	2024
rapidphylo: Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method (Version 0.1.2)	2022
recluster: Ordination Methods for the Analysis of Beta-Diversity Indices (Version 2.9)	2013
rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics (Version 1.0.2)	2016
scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale (Version 1.2.0)	2022
shipunov: Miscellaneous Functions from Alexey Shipunov (Version 1.17.1)	2019
sketching: Sketching of Data via Random Subspace Embeddings (Version 0.1.2)	2022
tracerer: Tracer from R (Version 2.2.3)	2018
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

RPKG Scholar presents a tabulation of an author's contribution in the development of R packages stored in the Comprehensive R Archive Network (CRAN). Within this site, we consider package dependencies (suggests,imports,depends,enhances) as citations because we believe that using one's package to develop another is tantamount to citing the author of the package being imported, suggested or enhanced.