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 22 articles )

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  1. Liebscher, Volkmar: New Gromov-inspired metrics on phylogenetic tree space (2018)
  2. 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)
  3. Baumer, Benjamin S.; Kaplan, Daniel T.; Horton, Nicholas J.: Modern data science with R (2017)
  4. Chen, Youhua: Impacts of phylogenetic dilution and concentration effects on species diversity and distribution patterns (2017)
  5. Julia Fukuyama: Adaptive gPCA: A method for structured dimensionality reduction (2017) arXiv
  6. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  7. Lin, Bo; Sturmfels, Bernd; Tang, Xiaoxian; Yoshida, Ruriko: Convexity in tree spaces (2017)
  8. Wicke, Kristina; Fischer, Mareike: Comparing the rankings obtained from two biodiversity indices: the fair proportion index and the Shapley value (2017)
  9. Xi, Jing; Xie, Jin; Yoshida, Ruriko: Distributions of topological tree metrics between a species tree and a gene tree (2017)
  10. Michael D. Karcher, Julia A. Palacios, Shiwei Lan, Vladimir N. Minin: phylodyn: an R package for phylodynamic simulation and inference (2016) arXiv
  11. Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp: RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R (2015) arXiv
  12. Jhwueng, Dwueng-Chwuan; Maroulas, Vasileios: Phylogenetic Ornstein-Uhlenbeck regression curves (2014)
  13. Swenson, Nathan G.: Functional and phylogenetic ecology in R (2014)
  14. Jiang, Xun; Dey, Dipak K.; Prunier, Rachel; Wilson, Adam M.; Holsinger, Kent E.: A new class of flexible link functions with application to species co-occurrence in Cape Floristic region (2013)
  15. Paradis, Emmanuel: Analysis of phylogenetics and evolution with R (2012)
  16. Borcard, Daniel; Gillet, François; Legendre, Pierre: Numerical ecology with R. (2011)
  17. Mariadassou, Mahendra; Robin, Stéphane; Vacher, Corinne: Uncovering latent structure in valued graphs: a variational approach (2010)
  18. Rahnenführer, Jörg: Book review of: R. Gentleman et al., Bioinformatics and computational biology solutions using R and bioconductor (2009)
  19. Claude, Julien: Morphometrics with R (2008)
  20. Nicholls, Geoff K.; Gray, Russell D.: Dated ancestral trees from binary trait data and their application to the diversification of languages (2008)

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