43 lines
2.3 KiB
Python
43 lines
2.3 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level 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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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-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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