48 lines
2.6 KiB
Python
48 lines
2.6 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class RApe(RPackage):
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"""Analyses of Phylogenetics and Evolution.
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Functions for reading, writing, plotting, and manipulating phylogenetic
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trees, analyses of comparative data in a phylogenetic framework, ancestral
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character analyses, analyses of diversification and macroevolution,
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computing distances from DNA sequences, reading and writing nucleotide
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sequences as well as importing from BioConductor, and several tools such as
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Mantel's test, generalized skyline plots, graphical exploration of
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phylogenetic data (alex, trex, kronoviz), estimation of absolute
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evolutionary rates and clock-like trees using mean path lengths and
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penalized likelihood, dating trees with non-contemporaneous sequences,
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translating DNA into AA sequences, and assessing sequence alignments.
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Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
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triangle methods, and several methods handling incomplete distance matrices
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(NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions
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call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results
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are returned into R."""
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cran = "ape"
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license("GPL-2.0-only OR GPL-3.0-only")
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version("5.8", sha256="24ce729979e1bcc60317e71e5100ce54156ceb7484917b0d64260f733ae84d24")
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version("5.7-1", sha256="8b09c71218d8aa629e43bc807b433a4e30a61847d91b2810e31c366f0fe5057a")
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version("5.6-2", sha256="9b62450a0390a1f07df007d348ad4cedcd814d42cb11c5a300ed33550fd41257")
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version("5.6-1", sha256="25401e036576eed1200e15bf68879ccd85611303a3508b989e15164cd4c0f7f7")
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version("5.4-1", sha256="f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4")
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version("5.3", sha256="08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23")
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version("5.2", sha256="27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415")
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version("5.1", sha256="b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e")
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version("5.0", sha256="c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960")
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version("4.1", sha256="935af5ddadcba832d3f9cc032a80fc1a2e627a7ed54ef5f3773f87e06374a924")
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depends_on("r@3.2:", type=("build", "run"))
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depends_on("r@3.2.0:", type=("build", "run"), when="@5.7-1:")
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depends_on("r-nlme", type=("build", "run"))
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depends_on("r-lattice", type=("build", "run"))
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depends_on("r-rcpp@0.12.0:", type=("build", "run"))
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depends_on("r-digest", type=("build", "run"), when="@5.7-1:")
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