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.

Type Size Name Uploaded Uploader Downloads Labels
conda 2.2 MB | osx-64/r-ape-5.3-r351hf99fc2c_0.tar.bz2  3 months and 2 days ago conda-forge 239 main
conda 2.3 MB | win-64/r-ape-5.3-r351h6115d3f_0.tar.bz2  3 months and 2 days ago conda-forge 157 main
conda 2.2 MB | linux-64/r-ape-5.3-r351h0357c0b_0.tar.bz2  3 months and 2 days ago conda-forge 1366 main
conda 2.2 MB | osx-64/r-ape-5.2-r351h466af19_0.tar.bz2  4 months and 15 hours ago conda-forge 84 main
conda 2.1 MB | linux-64/r-ape-5.2-r351h29659fb_0.tar.bz2  4 months and 17 hours ago conda-forge 643 main
conda 2.3 MB | win-64/r-ape-5.2-r351h6115d3f_0.tar.bz2  4 months and 17 hours ago conda-forge 176 main
conda 2.1 MB | linux-64/r-ape-5.1-r351h29659fb_1002.tar.bz2  7 months and 2 days ago conda-forge 1625 main gcc7
conda 2.2 MB | win-64/r-ape-5.1-r351h6115d3f_1002.tar.bz2  7 months and 2 days ago conda-forge 334 main cf201901
conda 2.1 MB | osx-64/r-ape-5.1-r351h466af19_1002.tar.bz2  7 months and 2 days ago conda-forge 178 main gcc7
conda 2.2 MB | win-64/r-ape-5.1-r351h6115d3f_2.tar.bz2  9 months and 5 days ago conda-forge 363 main cf201901
conda 1.6 MB | win-64/r-ape-5.1-r341h6115d3f_2.tar.bz2  9 months and 5 days ago conda-forge 354 main cf201901
conda 2.1 MB | osx-64/r-ape-5.1-r351h9d2a408_2.tar.bz2  9 months and 5 days ago conda-forge 249 main cf201901
conda 2.2 MB | linux-64/r-ape-5.1-r351h9d2a408_2.tar.bz2  9 months and 5 days ago conda-forge 1843 main cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r341h9d2a408_2.tar.bz2  9 months and 5 days ago conda-forge 2708 main cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r341h9d2a408_2.tar.bz2  9 months and 5 days ago conda-forge 189 main cf201901
conda 1.6 MB | win-64/r-ape-5.1-r341hca4a3dc_1.tar.bz2  10 months and 16 days ago conda-forge 421 main cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r341hfc679d8_1.tar.bz2  10 months and 17 days ago conda-forge 62 main cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r341hfc679d8_1.tar.bz2  10 months and 17 days ago conda-forge 1252 main cf201901
conda 1.6 MB | win-64/r-ape-5.1-r3.3.2_0.tar.bz2  1 year and 2 months ago conda-forge 463 main cf201901
conda 1.6 MB | win-64/r-ape-5.1-r3.4.1_0.tar.bz2  1 year and 2 months ago conda-forge 489 main cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r3.4.1_0.tar.bz2  1 year and 2 months ago conda-forge 252 main cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r3.3.2_0.tar.bz2  1 year and 2 months ago conda-forge 88 main cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r3.4.1_0.tar.bz2  1 year and 2 months ago conda-forge 1842 main cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r3.4.1_0.tar.bz2  1 year and 2 months ago conda-forge 709 broken
conda 1.5 MB | linux-64/r-ape-5.1-r3.3.2_0.tar.bz2  1 year and 2 months ago conda-forge 1068 main cf201901
conda 1.4 MB | osx-64/r-ape-5.0-r3.4.1_0.tar.bz2  1 year and 7 months ago conda-forge 200 main cf201901
conda 1.4 MB | osx-64/r-ape-5.0-r3.3.2_0.tar.bz2  1 year and 7 months ago conda-forge 63 main cf201901
conda 1.6 MB | win-64/r-ape-5.0-r3.4.1_0.tar.bz2  1 year and 7 months ago conda-forge 604 main cf201901
conda 1.6 MB | win-64/r-ape-5.0-r3.3.2_0.tar.bz2  1 year and 7 months ago conda-forge 550 main cf201901
conda 1.5 MB | win-64/r-ape-4.1-r3.4.1_0.tar.bz2  1 year and 7 months ago conda-forge 493 main cf201901
conda 1.5 MB | linux-64/r-ape-5.0-r3.3.2_0.tar.bz2  1 year and 7 months ago conda-forge 1277 main cf201901
conda 1.5 MB | linux-64/r-ape-5.0-r3.4.1_0.tar.bz2  1 year and 7 months ago conda-forge 1830 main cf201901
conda 1.3 MB | osx-64/r-ape-4.1-r3.4.1_0.tar.bz2  1 year and 9 months ago conda-forge 61 main cf201901
conda 1.3 MB | linux-64/r-ape-4.1-r3.4.1_0.tar.bz2  1 year and 10 months ago conda-forge 1275 main cf201901
conda 1.5 MB | win-64/r-ape-4.1-r3.3.2_0.tar.bz2  2 years and 1 month ago conda-forge 529 main cf201901
conda 1.3 MB | osx-64/r-ape-4.1-r3.3.2_0.tar.bz2  2 years and 1 month ago conda-forge 67 main cf201901
conda 1.3 MB | linux-64/r-ape-4.1-r3.3.2_0.tar.bz2  2 years and 1 month ago conda-forge 1432 main cf201901
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