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phangorn

phangorn: Phylogenetic analysis in R. Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)

Keywords for this software

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  • R package
  • JOSS
  • Journal Open Source Software
  • R
  • Ornstein-Uhlenbeck process
  • trait evolution
  • Hidden Markov Models
  • species tree
  • CIR process
  • regularization
  • phylogenetics
  • gene tree
  • HMM
  • tree reconstruction
  • Brownian motion
  • Evolutionary Analysis
  • approximate Bayesian computation
  • EggNOG database
  • bioinformatics
  • Dendrograms
  • Gaussian process
  • phylogenetic reconstruction
  • maximum likelihood estimator
  • phylogenetic comparative analysis
  • genetic data

  • URL: cran.r-project.org/web...
  • Code
  • InternetArchive
  • Manual: cran.r-project.org/web...
  • Authors: Klaus Schliep, Emmanuel Paradis
  • Dependencies: R

  • Add information on this software.


  • Related software:
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  • phytools
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  • Graphviz
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  • Phylen
  • PHYLIP
  • qPR
  • OUOUCIR
  • MrBayes
  • GEIGER
  • TreeFix
  • EasyABC
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References in zbMATH (referenced in 6 articles )

Showing results 1 to 6 of 6.
y Sorted by year (citations)

  1. Jhwueng, Dwueng-Chwuan: Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation approach (2020)
  2. Dinh, Vu; Ho, Lam Si Tung; Suchard, Marc A.; Matsen, Frederick A. IV: Consistency and convergence rate of phylogenetic inference via regularization (2018)
  3. Ignacio Ferres; Gregorio Iraola: Phylen: automatic phylogenetic reconstruction using the EggNOG database (2018) not zbMATH
  4. Shaun Wilkinson, Simon Davy: phylogram: an R package for phylogenetic analysis with nested lists (2018) not zbMATH
  5. Paradis, Emmanuel: Analysis of phylogenetics and evolution with R (2012)
  6. Schliep, Klaus Peter: Phangorn: phylogenetic analysis in R (2011) ioport

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  • MSC classification / top
    • Top MSC classes
      • 05 Combinatorics
      • 60 Probability theory and...
      • 62 Statistics
      • 92 Applications of...

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