phangorn: Phylogenetic Reconstruction and Analysis

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

2.11.1 Version

0 Citations

18 Authors

Referenced by ⇅	Year
babette: Control "BEAST2" (Version 2.3.3)	2020
liayson: Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes (Version 1.0.5)	2018
mcbette: Model Comparison Using "babette" (Version 1.15.2)	2020
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
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 2.0)	2019
MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis (Version 0.7.10)	2024
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
POMS: Phylogenetic Organization of Metagenomic Signals (Version 1.0.1)	2022
Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.5.0)	2021
Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures (Version 1.2.6)	2019
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
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 1.2.0)	2023
TreeDist: Calculate and Map Distances Between Phylogenetic Trees (Version 2.7.0)	2020
TreeSearch: Phylogenetic Analysis with Discrete Character Data (Version 1.5.0)	2017
TreeTools: Create, Modify and Analyse Phylogenetic Trees (Version 1.10.0)	2019
ape: Analyses of Phylogenetics and Evolution (Version 5.8)	2002
apex: Phylogenetic Methods for Multiple Gene Data (Version 1.0.6)	2015
beastier: Call 'BEAST2' (Version 2.5)	2019
coalescentMCMC: MCMC Algorithms for the Coalescent (Version 0.4-4)	2012
corHMM: Hidden Markov Models of Character Evolution (Version 2.8)	2013
datelife: Scientific Data on Time of Lineage Divergence for Your Taxa (Version 0.6.8)	2022
dendextend: Extending 'dendrogram' Functionality in R (Version 1.17.1)	2014
dispRity: Measuring Disparity (Version 1.8)	2018
dowser: B Cell Receptor Phylogenetics Toolkit (Version 2.1.0)	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 0.0.11)	2014
markophylo: Markov Chain Models for Phylogenetic Trees (Version 1.0.9)	2015
microbial: Do 16s Data Analysis and Generate Figures (Version 0.0.20)	2020
nodeSub: Simulate DNA Alignments Using Node Substitutions (Version 1.2.8)	2022
paleotree: Paleontological and Phylogenetic Analyses of Evolution (Version 3.4.5)	2012
pcmabc: Approximate Bayesian Computations for Phylogenetic Comparative Methods (Version 1.1.3)	2019
phyloregion: Biogeographic Regionalization and Macroecology (Version 1.0.8)	2020
phytools: Phylogenetic Tools for Comparative Biology (and Other Things) (Version 2.1-1)	2011
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
taxize: Taxonomic Information from Around the Web (Version 0.9.100)	2012
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

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