Package: ape 5.8
ape: Analyses of Phylogenetics and Evolution
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.
Authors:
ape_5.8.tar.gz
ape_5.8.tar.gz(r-4.5-noble)ape_5.8.tar.gz(r-4.4-noble)
ape_5.8.tgz(r-4.4-emscripten)ape_5.8.tgz(r-4.3-emscripten)
ape.pdf |ape.html✨
ape/json (API)
NEWS
# Install 'ape' in R: |
install.packages('ape', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/emmanuelparadis/ape/issues
- HP.links - Test of host-parasite coevolution
- bird.families - Phylogeny of the Families of Birds From Sibley and Ahlquist
- bird.orders - Phylogeny of the Orders of Birds From Sibley and Ahlquist
- carnivora - Carnivora body sizes and life history traits
- chiroptera - Bat Phylogeny
- cynipids - NEXUS Data Example
- gopher.D - Test of host-parasite coevolution
- hivtree.newick - Phylogenetic Tree of 193 HIV-1 Sequences
- hivtree.table - Phylogenetic Tree of 193 HIV-1 Sequences
- lice.D - Test of host-parasite coevolution
- lmorigin.ex1 - Multiple regression through the origin
- lmorigin.ex2 - Multiple regression through the origin
- mat3 - Three Matrices
- mat5M3ID - Five Trees
- mat5Mrand - Five Independent Trees
- woodmouse - Cytochrome b Gene Sequences of Woodmice
Last updated 8 months agofrom:71a1c7f72d. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 07 2024 |
R-4.5-linux-x86_64 | OK | Dec 07 2024 |
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Drawing Phylogenies
Rendered fromDrawingPhylogenies.Rnw
usingutils::Sweave
on Dec 07 2024.Last update: 2024-04-11
Started: 2021-04-25
Moran's I
Rendered fromMoranI.Rnw
usingutils::Sweave
on Dec 07 2024.Last update: 2021-04-25
Started: 2013-07-19
Random Topology
Rendered fromRandomTopologies.Rnw
usingutils::Sweave
on Dec 07 2024.Last update: 2024-04-11
Started: 2021-04-25