Balík: r-cran-ape (5.4-1-1)

[ Zdroj: r-cran-ape  ]

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.

Značky: Software Development: Vývoj v GNU R, Pole: Statistics, Implementované v: GNU R

Ostatné balíky súvisiace s balíkom r-cran-ape

• dep: libc6 (>= 2.29)

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  podporná knižnica GCC

• dep: liblapack3

  knižnica rutín lineárnej algebry, verzia 3 - zdieľaná knižnica

  alebo liblapack.so.3

  virtuálny balík poskytovaný balíkom libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libstdc++6 (>= 5.2)

  štandardná knižnica C++ GNU v3

• dep: r-api-4.0

  virtuálny balík poskytovaný balíkom r-base-core

• dep: r-base-core (>= 4.0.2-1)

  jadro GNU R na štatistické výpočty a grafický systém

• dep: r-cran-lattice

  balík GNU R pre grafiku „Trellis“

• dep: r-cran-nlme

  balík GNU R na (ne-)lineárne modely zmiešaných efektov

• dep: r-cran-rcpp (>= 0.12.0)

  balík GNU R na hladkú integráciu R a C++

• sug: clustalw

  globálne viacnásobné zarovnávanie sekvencií nukleotidov alebo peptidov

• 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

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