Package: EnvNJ
Type: Package
Title: Whole Genome Phylogenies Using Sequence Environments
Version: 0.1.3
Authors@R: 
    person(given = "Juan Carlos",
           family = "Aledo",
           role = c("aut", "cre"),
           email = "caledo@uma.es",
           comment = c(ORCID = "0000-0002-3497-9945"))
Description: 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.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
Depends: R (>= 4.0.0)
Imports: ape, bio3d, graphics, phangorn, philentropy, seqinr, stringr
Suggests: testthat
NeedsCompilation: no
Packaged: 2026-07-14 07:25:19 UTC; root
Author: Juan Carlos Aledo [aut, cre]
        (<https://orcid.org/0000-0002-3497-9945>)
Maintainer: Juan Carlos Aledo <caledo@uma.es>
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev zlib1g-dev
Repository: https://jcaledo.r-universe.dev
Date/Publication: 2021-09-27 09:50:02 UTC
RemoteUrl: https://github.com/cran/EnvNJ
RemoteRef: HEAD
RemoteSha: e5e6a81a21b56cd9eabe67f964b1cea227303b8d