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# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class RApe(RPackage):
"""Analyses of Phylogenetics and Evolution.
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."""
cran = "ape"
license("GPL-2.0-only OR GPL-3.0-only")
version("5.7-1", sha256="8b09c71218d8aa629e43bc807b433a4e30a61847d91b2810e31c366f0fe5057a")
version("5.6-2", sha256="9b62450a0390a1f07df007d348ad4cedcd814d42cb11c5a300ed33550fd41257")
version("5.6-1", sha256="25401e036576eed1200e15bf68879ccd85611303a3508b989e15164cd4c0f7f7")
version("5.4-1", sha256="f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4")
version("5.3", sha256="08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23")
version("5.2", sha256="27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415")
version("5.1", sha256="b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e")
version("5.0", sha256="c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960")
version("4.1", sha256="935af5ddadcba832d3f9cc032a80fc1a2e627a7ed54ef5f3773f87e06374a924")
depends_on("r@3.2:", type=("build", "run"))
depends_on("r@3.2.0:", type=("build", "run"), when="@5.7-1:")
depends_on("r-nlme", type=("build", "run"))
depends_on("r-lattice", type=("build", "run"))
depends_on("r-rcpp@0.12.0:", type=("build", "run"))
depends_on("r-digest", type=("build", "run"), when="@5.7-1:")
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