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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 asmeurer / r-ape
Type Size Name Uploaded Downloads Labels
conda 3.0 MB | linux-64/r-ape-5.7_1-r43h884c59f_0.tar.bz2  1 year and 6 months ago 1122 main
conda 3.2 MB | linux-64/r-ape-5.6_2-r42h884c59f_0.tar.bz2  3 years and 1 month ago 1346 main
conda 2.3 MB | win-64/r-ape-5.3-r36h6115d3f_0.tar.bz2  5 years and 4 months ago 114 main
conda 2.2 MB | win-64/r-ape-5.1-r351h6f4ce42_0.tar.bz2  5 years and 4 months ago 84 main
conda 2.8 MB | win-64/r-ape-5.1-mro351_0.tar.bz2  5 years and 4 months ago 79 main
conda 1.6 MB | win-64/r-ape-5.0-r343h889e2dd_0.tar.bz2  5 years and 4 months ago 73 main
conda 2.0 MB | win-64/r-ape-5.0-mro343h889e2dd_0.tar.bz2  5 years and 4 months ago 78 main
conda 1.5 MB | win-64/r-ape-4.1-r342h20b4ec8_0.tar.bz2  5 years and 4 months ago 80 main
conda 1.5 MB | win-64/r-ape-4.1-r3.4.1_0.tar.bz2  5 years and 4 months ago 81 main
conda 1.5 MB | win-64/r-ape-4.0-r3.3.2_0.tar.bz2  5 years and 4 months ago 81 main
conda 1.4 MB | win-64/r-ape-3.5-r3.3.1_0.tar.bz2  5 years and 4 months ago 73 main
conda 1.4 MB | win-64/r-ape-3.4-r3.3.0_0.tar.bz2  5 years and 4 months ago 87 main
conda 1.4 MB | win-64/r-ape-3.4-r3.2.4_0.tar.bz2  5 years and 4 months ago 84 main
conda 2.3 MB | win-32/r-ape-5.3-r36h6115d3f_0.tar.bz2  5 years and 4 months ago 29 main
conda 2.3 MB | win-32/r-ape-5.1-r351h6f4ce42_0.tar.bz2  5 years and 4 months ago 29 main
conda 1.6 MB | win-32/r-ape-5.0-r343h889e2dd_0.tar.bz2  5 years and 4 months ago 30 main
conda 1.5 MB | win-32/r-ape-4.1-r3.4.1_0.tar.bz2  5 years and 4 months ago 27 main
conda 1.5 MB | win-32/r-ape-4.1-r342h8924321_0.tar.bz2  5 years and 4 months ago 33 main
conda 1.5 MB | win-32/r-ape-4.0-r3.3.2_0.tar.bz2  5 years and 4 months ago 29 main
conda 1.4 MB | win-32/r-ape-3.5-r3.3.1_0.tar.bz2  5 years and 4 months ago 28 main
conda 1.4 MB | win-32/r-ape-3.4-r3.3.0_0.tar.bz2  5 years and 4 months ago 33 main
conda 1.4 MB | win-32/r-ape-3.4-r3.2.4_0.tar.bz2  5 years and 4 months ago 28 main
conda 2.2 MB | osx-64/r-ape-5.3-r36h466af19_0.tar.bz2  5 years and 4 months ago 202 main
conda 2.1 MB | osx-64/r-ape-5.1-r351h32998d9_0.tar.bz2  5 years and 4 months ago 77 main
conda 2.1 MB | osx-64/r-ape-5.1-r350h1104f25_0.tar.bz2  5 years and 4 months ago 51 main

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