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) . 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.


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0.1.3 by Juan Carlos Aledo, 2 months ago

Browse source code at https://github.com/cran/EnvNJ

Authors: Juan Carlos Aledo [aut, cre]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports ape, bio3d, graphics, phangorn, philentropy, seqinr, stringr

Suggests testthat

See at CRAN