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
Author: Juan Carlos Aledo ORCID iD [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

Downloads:

Reference manual: EnvNJ.pdf
Package source: EnvNJ_0.1.3.tar.gz
Windows binaries: r-devel: EnvNJ_0.1.2.zip, r-release: EnvNJ_0.1.2.zip, r-oldrel: EnvNJ_0.1.2.zip
macOS binaries: r-release (arm64): EnvNJ_0.1.2.tgz, r-release (x86_64): EnvNJ_0.1.2.tgz, r-oldrel: EnvNJ_0.1.2.tgz
Old sources: EnvNJ archive

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