Whole Genome Phylogenies Using Sequence Environments R package EnvNJ version 0.1.3 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. Software Depends: R (>= 4.0.0) Imports: ape, bio3d, graphics, phangorn, philentropy, seqinr, stringr Suggests: testthat Juan Carlos Aledo <caledo@uma.es> Comprehensive R Archive Network (CRAN) Juan Carlos Aledo [aut, cre] (ORCID: <https://orcid.org/0000-0002-3497-9945>) GPL (>= 2) 2021-09-27 application/tgz https://CRAN.R-project.org/package=EnvNJ doi:10.32614/CRAN.package.EnvNJ