EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.

Version:	0.1.3
Depends:	R (≥ 4.0.0)
Imports:	ape, bio3d, graphics, phangorn, philentropy, seqinr, stringr
Suggests:	testthat
Published:	2021-09-27
DOI:	10.32614/CRAN.package.EnvNJ
Author:	Juan Carlos Aledo [aut, cre]
Maintainer:	Juan Carlos Aledo <caledo at uma.es>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
Materials:	NEWS
CRAN checks:	EnvNJ results

Documentation:

Reference manual:

EnvNJ.html , EnvNJ.pdf

Downloads:

Package source:	EnvNJ_0.1.3.tar.gz
Windows binaries:	r-devel: EnvNJ_0.1.3.zip, r-release: EnvNJ_0.1.3.zip, r-oldrel: EnvNJ_0.1.3.zip
macOS binaries:	r-release (arm64): EnvNJ_0.1.3.tgz, r-oldrel (arm64): EnvNJ_0.1.3.tgz, r-release (x86_64): EnvNJ_0.1.3.tgz, r-oldrel (x86_64): EnvNJ_0.1.3.tgz
Old sources:	EnvNJ archive

Linking:

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