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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 2.7 MB | osx-arm64/r-ape-5.8_1-r43h1968f39_1.conda  27 days and 21 hours ago 43 main
conda 2.8 MB | win-64/r-ape-5.8_1-r43hac2c72c_1.conda  27 days and 21 hours ago 69 main
conda 2.8 MB | win-64/r-ape-5.8_1-r44hac2c72c_1.conda  27 days and 21 hours ago 66 main
conda 2.8 MB | osx-arm64/r-ape-5.8_1-r44h1968f39_1.conda  27 days and 21 hours ago 98 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r44h440a4f6_1.conda  27 days and 21 hours ago 23 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r44h1934be7_1.conda  27 days and 21 hours ago 119 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r43h9e3ff46_1.conda  27 days and 21 hours ago 56 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r43h1934be7_1.conda  27 days and 21 hours ago 413 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r43h3704496_1.conda  27 days and 21 hours ago 2388 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r44h9e3ff46_1.conda  27 days and 21 hours ago 124 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r44h3704496_1.conda  27 days and 21 hours ago 4715 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r43h440a4f6_1.conda  27 days and 21 hours ago 23 main
conda 2.8 MB | win-64/r-ape-5.8_1-r44h3dc9324_0.conda  8 months and 13 days ago 421 main
conda 2.7 MB | win-64/r-ape-5.8_1-r43h3dc9324_0.conda  8 months and 13 days ago 359 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r44h69b9914_0.conda  8 months and 13 days ago 190 main
conda 2.8 MB | osx-arm64/r-ape-5.8_1-r44h91c3ca0_0.conda  8 months and 13 days ago 652 main
conda 2.7 MB | osx-arm64/r-ape-5.8_1-r43h91c3ca0_0.conda  8 months and 13 days ago 364 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r44h4a69edb_0.conda  8 months and 13 days ago 764 main
conda 2.8 MB | osx-64/r-ape-5.8_1-r43h4a69edb_0.conda  8 months and 13 days ago 3367 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r43h9eb5c89_0.conda  8 months and 13 days ago 570 main
conda 2.8 MB | linux-ppc64le/r-ape-5.8_1-r43h69b9914_0.conda  8 months and 13 days ago 217 main
conda 2.8 MB | linux-aarch64/r-ape-5.8_1-r44h9eb5c89_0.conda  8 months and 13 days ago 641 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r43hb79369c_0.conda  8 months and 13 days ago 19590 main
conda 2.8 MB | linux-64/r-ape-5.8_1-r44hb79369c_0.conda  8 months and 13 days ago 16172 main
conda 2.8 MB | win-64/r-ape-5.8-r44h3dc9324_1.conda  1 year and 1 month ago 536 main

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