Package: r-cran-ape (5.8-1) [debports]

[ Source:  ]

GNU R package for Analyses of Phylogenetics and Evolution

This package 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 DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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.

Other Packages Related to r-cran-ape

• dep: libc6 (>= 2.29)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc-s4 (>= 4.1.1)

  GCC support library

• dep: liblapack3

  Library of linear algebra routines 3 - shared version

  or liblapack.so.3

  virtual package provided by libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

• dep: r-api-4.0

  virtual package provided by r-base-core

• dep: r-cran-digest

  GNU R package for 'hash digest' of R data structures

• dep: r-cran-lattice

  GNU R package for 'Trellis' graphics

• dep: r-cran-nlme

  GNU R package for (non-)linear mixed effects models

• dep: r-cran-rcpp (>= 0.12.0)

  GNU R package for Seamless R and C++ Integration

• rec: r-cran-phangorn

  GNU R package for phylogenetic analysis

• sug: clustalw

  global multiple nucleotide or peptide sequence alignment

• sug: muscle

  Multiple alignment program of protein sequences

• sug: phyml

  Phylogenetic estimation using Maximum Likelihood

• sug: r-cran-expm

  GNU R Computation of the matrix exponential and related quantities

• sug: r-cran-gee

  Generalized Estimation Equation Solver

• sug: r-cran-igraph

  GNU R network analysis and visualization

• sug: t-coffee

  Multiple Sequence Alignment

Download r-cran-ape

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Architecture	Package Size	Installed Size	Files
hppa (unofficial port)	2,848.5 kB	3,700.0 kB	[list of files]