22df09315f
* r-igraph: find old packages in the archive Fixes #6104. * r-irlba: find old packages in the archive Fixes #6101. * r-lazyeval: find old packages in the archive Fixes #6102. * packages: set list_url for all packages hosted on CRAN * packages: consistently use the CRAN archive URLs
52 lines
2.6 KiB
Python
52 lines
2.6 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RApe(RPackage):
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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
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as 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
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matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
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functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
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whose results are returned into R."""
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homepage = "http://ape-package.ird.fr/"
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url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
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list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
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version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
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depends_on('r@3.2:')
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