aa.at                   Residue Found at the Requested Position
aa.comp                 Amino Acid Composition
aaf                     Compute the Frequency of Each Amino Acid in
                        Each Species
bovids                  13 orthologous mtDNA-encoded proteins of 11
                        bovine species.
cos2dis                 Convert Cosines Between Vectors into Pairwise
                        Dissimilarities
d.phy2df                Convert a Phylip Distance Matrix into a
                        DataFrame
df2fasta                Convert Dataframe into Fasta File
env.extract             Sequence Environment Around a Given Position
env.fasta               Build Trees Based on the Environment Around the
                        Indicated Amino Acid(s)
env.matrices            Environment Matrices
env.sp                  Extract the Sequence Environments
envfascpp               Convert Fasta Files into Environment Vectors
envnj                   Build Trees Based on the Environment Around the
                        Indicated Amino Acid(s)
fastaconc               Concatenate Fasta Files in a Single
                        Multispecies Fasta File
metrics                 Pairwise Vector Dissimilarities
msa.merge               Carry Out a MSA of a Set of Different
                        Orthologous Proteins
msa.tree                Infer a tree based on a MSA
ncd                     Compute Normalized Compression Distances
ncdnj                   Compute a Distance Matrix Using Normalized
                        Compression Distance
ngraMatrix              Compute n-Gram Frequencies Dataframe
ngram                   Compute n-Gram Frequencies Vector
otu.space               Compute the Matrix Representing the Species
                        Vector Subspace
otu.vector              Convert a Set of Sequence Environments into a
                        Vector
reyes                   13 orthologous mtDNA-encoded proteins of 34
                        mammalian species.
svdgram                 Compute Phylogenetic Trees Using an n-Gram and
                        SVD Approach
vcos                    Compute Pairwise Cosines of the Angles Between
                        Vectors
vdis                    Compute Pairwise Distances Between Vectors
vect2tree               Convert a Set of Vectors into a Tree
vtree                   Build a Tree When Species Are Encoded by n-Dim
                        Vectors
