R package ape: Analyses of Phylogenetics and Evolution , ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel’s test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R. (Source: http://cran.r-project.org/web/packages)

References in zbMATH (referenced in 46 articles )

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  1. Jhwueng, Dwueng-Chwuan: Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation approach (2020)
  2. Fukuyama, Julia: Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data (2019)
  3. Ge, Li; Liu, Jiaguo; Zhang, Yusen; Dehmer, Matthias: Identifying anticancer peptides by using a generalized chaos game representation (2019)
  4. Monod, Anthea; Kališnik, Sara; Patiño-Galindo, Juan Ángel; Crawford, Lorin: Tropical sufficient statistics for persistent homology (2019)
  5. Royer-Carenzi, Manuela; Didier, Gilles: Testing for correlation between traits under directional evolution (2019)
  6. Tahir, Daniah; Glémin, Sylvain; Lascoux, Martin; Kaj, Ingemar: Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree (2019)
  7. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  8. Bartoszek, Krzysztof: Exact and approximate limit behaviour of the Yule tree’s cophenetic index (2018)
  9. Bivand, Roger S.; Wong, David W. S.: Comparing implementations of global and local indicators of spatial association (2018)
  10. Borcard, Daniel; Gillet, François; Legendre, Pierre: Numerical ecology with R (2018)
  11. Chris Groendyke; David Welch: epinet: An R Package to Analyze Epidemics Spread across Contact Networks (2018) not zbMATH
  12. Ignacio Ferres; Gregorio Iraola: Phylen: automatic phylogenetic reconstruction using the EggNOG database (2018) not zbMATH
  13. Jin Zhu, Wenliang Pan, Wei Zheng, Xueqin Wang: Ball: An R package for detecting distribution difference and association in metric spaces (2018) arXiv
  14. Liebscher, Volkmar: New Gromov-inspired metrics on phylogenetic tree space (2018)
  15. Lin, Bo; Yoshida, Ruriko: Tropical Fermat-Weber points (2018)
  16. Podani, János; Pavoine, Sandrine; Ricotta, Carlo: A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data (2018)
  17. Shaun Wilkinson, Simon Davy: phylogram: an R package for phylogenetic analysis with nested lists (2018) not zbMATH
  18. Venelin Mitov; Tanja Stadler: Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library (2018) not zbMATH
  19. Ané, Cécile; Ho, Lam Si Tung; Roch, Sebastien: Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree (2017)
  20. Baumer, Benjamin S.; Kaplan, Daniel T.; Horton, Nicholas J.: Modern data science with R (2017)

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