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: 2021-09-27 10:36:44 UTC; JCA
Author: Juan Carlos Aledo [aut, cre] (<https://orcid.org/0000-0002-3497-9945>)
Maintainer: Juan Carlos Aledo <caledo@uma.es>
Repository: CRAN
Date/Publication: 2021-09-27 10:50:02 UTC
Built: R 4.6.0; ; 2026-04-28 02:54:18 UTC; unix
