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) <10.1093>. 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.10.1093>