{ "_id": "6a1f527cb401979e7342a005", "Package": "ape", "Version": "5.8-3", "Date": "2026-06-02", "Title": "Analyses of Phylogenetics and Evolution", "Authors@R": "c(person(\"Emmanuel\", \"Paradis\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Emmanuel.Paradis@ird.fr\", comment = c(ORCID = \"0000-0003-3092-2199\")),\nperson(\"Simon\", \"Blomberg\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-1062-0839\")),\nperson(\"Ben\", \"Bolker\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-2127-0443\")),\nperson(\"Joseph\", \"Brown\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3835-8062\")),\nperson(\"Santiago\", \"Claramunt\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-8926-5974\")),\nperson(\"Julien\", \"Claude\", role = c(\"aut\", \"cph\"), , comment = c(ORCID = \"0000-0002-9267-1228\")),\nperson(\"Hoa Sien\", \"Cuong\", role = c(\"aut\", \"cph\")),\nperson(\"Richard\", \"Desper\", role = c(\"aut\", \"cph\")),\nperson(\"Gilles\", \"Didier\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-0596-9112\")),\nperson(\"Benoit\", \"Durand\", role = c(\"aut\", \"cph\")),\nperson(\"Julien\", \"Dutheil\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7753-4121\")),\nperson(\"RJ\", \"Ewing\", role = c(\"aut\", \"cph\")),\nperson(\"Olivier\", \"Gascuel\", role = c(\"aut\", \"cph\")),\nperson(\"Thomas\", \"Guillerme\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-4325-1275\")),\nperson(\"Christoph\", \"Heibl\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-7655-3299\")),\nperson(\"Anthony\", \"Ives\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-9375-9523\")),\nperson(\"Bradley\", \"Jones\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-4498-1069\")),\nperson(\"Franz\", \"Krah\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7866-7508\")),\nperson(\"Daniel\", \"Lawson\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-5311-6213\")),\nperson(\"Vincent\", \"Lefort\", role = c(\"aut\", \"cph\")),\nperson(\"Pierre\", \"Legendre\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3838-3305\")),\nperson(\"Jim\", \"Lemon\", role = c(\"aut\", \"cph\")),\nperson(\"Guillaume\", \"Louvel\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-7745-0785\")),\nperson(\"Federico\", \"Marotta\", role = c(\"aut\", \"cph\")),\nperson(\"Eric\", \"Marcon\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-5249-321X\")),\nperson(\"Rosemary\", \"McCloskey\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-9772-8553\")),\nperson(\"Johan\", \"Nylander\", role = c(\"aut\", \"cph\")),\nperson(\"Rainer\", \"Opgen-Rhein\", role = c(\"aut\", \"cph\")),\nperson(\"Andrei-Alin\", \"Popescu\", role = c(\"aut\", \"cph\")),\nperson(\"Manuela\", \"Royer-Carenzi\", role = c(\"aut\", \"cph\")),\nperson(\"Klaus\", \"Schliep\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-2941-0161\")),\nperson(\"Korbinian\", \"Strimmer\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7917-2056\")),\nperson(\"Damien\", \"de Vienne\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-9532-5251\")))", "VignetteBuilder": "utils, knitr", "ZipData": "no", "Description": "Functions for reading, writing, plotting, and manipulating\nphylogenetic trees, analyses of comparative data in a\nphylogenetic framework, ancestral character analyses, analyses\nof diversification and macroevolution, computing distances from\nDNA sequences, reading and writing nucleotide sequences as well\nas importing from BioConductor, and several tools such as\nMantel's test, generalized skyline plots, graphical exploration\nof phylogenetic data (alex, trex, kronoviz), estimation of\nabsolute evolutionary rates and clock-like trees using mean\npath lengths and penalized likelihood, dating trees with\nnon-contemporaneous sequences, translating DNA into AA\nsequences, and assessing sequence alignments. Phylogeny\nestimation can be done with the NJ, BIONJ, ME, MVR, SDM, and\ntriangle methods, and several methods handling incomplete\ndistance matrices (NJ*, BIONJ*, MVR*, and the corresponding\ntriangle method). Some functions call external applications\n(PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are\nreturned into R.", "License": "GPL-2 | GPL-3", "URL": "https://github.com/emmanuelparadis/ape", "BugReports": "https://github.com/emmanuelparadis/ape/issues", "Encoding": "UTF-8", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2026-06-02 19:47:59 UTC", "RemoteUrl": "https://github.com/emmanuelparadis/ape", "RemoteRef": "HEAD", "RemoteSha": "53a291ccf10efc8d061cc7cfd17370be0eeacb1c", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 21:51:43 UTC", "User": "root" }, "Author": "Emmanuel Paradis [aut, cre, cph] (ORCID:\n),\nSimon Blomberg [aut, cph] (ORCID:\n),\nBen Bolker [aut, cph] (ORCID: ),\nJoseph Brown [aut, cph] (ORCID:\n),\nSantiago Claramunt [aut, cph] (ORCID:\n),\nJulien Claude [aut, cph] (ORCID:\n),\nHoa Sien Cuong [aut, cph],\nRichard Desper [aut, cph],\nGilles Didier [aut, cph] (ORCID:\n),\nBenoit Durand [aut, cph],\nJulien Dutheil [aut, cph] (ORCID:\n),\nRJ Ewing [aut, cph],\nOlivier Gascuel [aut, cph],\nThomas Guillerme [aut, cph] (ORCID:\n),\nChristoph Heibl [aut, cph] (ORCID:\n),\nAnthony Ives [aut, cph] (ORCID:\n),\nBradley Jones [aut, cph] (ORCID:\n),\nFranz Krah [aut, cph] (ORCID: ),\nDaniel Lawson [aut, cph] (ORCID:\n),\nVincent Lefort [aut, cph],\nPierre Legendre [aut, cph] (ORCID:\n),\nJim Lemon [aut, cph],\nGuillaume Louvel [aut, cph] (ORCID:\n),\nFederico Marotta [aut, cph],\nEric Marcon [aut, cph] (ORCID: ),\nRosemary McCloskey [aut, cph] (ORCID:\n),\nJohan Nylander [aut, cph],\nRainer Opgen-Rhein [aut, cph],\nAndrei-Alin Popescu [aut, cph],\nManuela Royer-Carenzi [aut, cph],\nKlaus Schliep [aut, cph] (ORCID:\n),\nKorbinian Strimmer [aut, cph] (ORCID:\n),\nDamien de Vienne [aut, cph] (ORCID:\n)", "Maintainer": "Emmanuel Paradis ", "MD5sum": "351e66cd007ddceb5587acef377866a1", "_user": "phylotastic", "_type": "src", "_file": "ape_5.8-3.tar.gz", "_fileid": 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