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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.

copied from cf-post-staging / r-ape
Type Size Name Uploaded Downloads Labels
conda 2.8 MB | osx-arm64/r-ape-5.8_1-r45hd057375_2.conda  27 days and 21 hours ago 58 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r45hefbd7a6_2.conda  27 days and 21 hours ago 122 main
conda 2.8 MB | osx-arm64/r-ape-5.8_1-r44hd057375_2.conda  27 days and 21 hours ago 128 main
conda 2.8 MB | win-64/r-ape-5.8_1-r45hac2c72c_2.conda  27 days and 21 hours ago 95 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r44hefbd7a6_2.conda  27 days and 21 hours ago 203 main
conda 2.8 MB | win-64/r-ape-5.8_1-r44hac2c72c_2.conda  27 days and 21 hours ago 105 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r44h440a4f6_2.conda  27 days and 21 hours ago 38 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r44h3704496_2.conda  27 days and 21 hours ago 3829 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r45h9e3ff46_2.conda  27 days and 21 hours ago 55 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r44h9e3ff46_2.conda  27 days and 21 hours ago 170 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r45h440a4f6_2.conda  27 days and 21 hours ago 34 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r45h3704496_2.conda  27 days and 21 hours ago 5995 main
conda 2.7 MB | osx-arm64/r-ape-5.8_1-r43h1968f39_1.conda  2 months and 4 days ago 65 main
conda 2.8 MB | win-64/r-ape-5.8_1-r43hac2c72c_1.conda  2 months and 4 days ago 95 main
conda 2.8 MB | win-64/r-ape-5.8_1-r44hac2c72c_1.conda  2 months and 4 days ago 81 main
conda 2.8 MB | osx-arm64/r-ape-5.8_1-r44h1968f39_1.conda  2 months and 4 days ago 137 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r44h440a4f6_1.conda  2 months and 4 days ago 32 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r44h1934be7_1.conda  2 months and 4 days ago 160 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r43h9e3ff46_1.conda  2 months and 4 days ago 84 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r43h1934be7_1.conda  2 months and 4 days ago 925 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r43h3704496_1.conda  2 months and 4 days ago 5903 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r44h9e3ff46_1.conda  2 months and 4 days ago 175 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r44h3704496_1.conda  2 months and 4 days ago 6421 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r43h440a4f6_1.conda  2 months and 4 days ago 36 main
conda 2.8 MB | win-64/r-ape-5.8_1-r44h3dc9324_0.conda  9 months and 19 days ago 426 main

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