aa_phychem_index        Amino acid mutation matrix
aaindex1                List of 571 Amino Acid Physicochemical Indexes
                        from AAindex Database
aaindex2                List of 94 Amino Acid Matrices from AAindex
aaindex3                Statistical protein contact potentials matrices
                        from AAindex ver.9.2
aln                     Simulated 'DNAStringSet' class object
aminoacid_dist          Distance Between Aminoacids in Terms of Codon
                        Distance
as.AutomorphismList     Methods for AutomorphismList-class Objects
aut3D                   Compute the Automorphisms of Mutational Events
                        Between two Codon Sequences Represented in
                        Z5^3.
autby_coef              Automorphisms between DNA Primate BRCA1 Genes
                        Grouped by Coefficients
autm                    Automorphisms between DNA Sequences from two
                        COVID-19 genomes
autm_3d                 Automorphisms between DNA Sequences from two
                        COVID-19 genomes
autm_z125               Automorphisms between DNA Sequences from two
                        COVID-19 genomes
automorphism_bycoef     Autmorphism Grouping by Coefficient
automorphism_prob       Autmorphism Probability
automorphismByRanges    Get the automorphisms by ranges.
automorphisms           Compute the Automorphisms of Mutational Events
                        Between two Codon Sequences Represented in a
                        Given Abelian group.
autZ125                 Compute the Automorphisms of Mutational Events
                        Between two Codon Sequences Represented in
                        Z125.
autZ5                   Compute the Automorphisms of Mutational Events
                        Between two Codon Sequences Represented in Z5.
autZ64                  Compute the Automorphisms of Mutational Events
                        Between two Codon Sequences Represented in Z64.
base_coord              DNA Sequences Methods
base2codon              Split a DNA sequence into codons
base2int                Replace bases with integers from Z4 and Z5
brca1_aln               Multiple Sequence Alignment (MSA) of Primate
                        BRCA1 DNA repair genes.
brca1_aln2              Multiple Sequence Alignment (MSA) of Primate
                        BRCA1 DNA repair genes.
brca1_autm              Automorphisms between DNA Sequences from
                        Primate BRCA1 Genes
brca1_autm2             Automorphisms between DNA Sequences from
                        Primate BRCA1 Genes
cdm_z64                 Codon Distance Matrices for the Standard
                        Genetic Code on Z4
codon_coord             Codon coordinates on a given a given Abelian
                        group representation.
codon_dist              Weighted Manhattan Distance Between Codons
codon_dist_matrix       Compute Codon Distance Matrix
codon_matrix            Codon Coordinate Matrix
conserved_regions       Conserved and Non-conserved Regions from a MSA
covid_aln               Pairwise Sequence Alignment (MSA) of COVID-19
                        genomes.
covid_autm              Automorphisms between DNA Sequences from two
                        COVID-19 genomes
cyc_aln                 Multiple Sequence Alignment (MSA) of Primate
                        Somatic Cytochrome C
cyc_autm                Automorphisms between DNA Sequences from
                        Primate Cytochrome C Genes
dna_phyche              Some Physicochemical Properties of DNA bases
dna_phychem             DNA numerical matrix
get_coord               DNA base/codon sequence and coordinates
                        represented on a given Abelian group.
get_mutscore            Get Mutation Score from an AAindex or a
                        Mutation/Distance Matrix
getAutomorphisms        Get Automorphisms
matrices                Get the Coordinate Representation from DNA
                        Sequences on Specified Abelian Group
mod                     Modulo Operation
modlineq                Modular System of Linear Equation Solver (MLE)
mut_type                Classification of DNA base mutations
peptide_phychem_index   Amino acid numerical matrix
seqranges               Get DNA sequence Ranges and Coordinates
                        representation on a given Abelian Group
slapply                 Apply a function over a list-like object
                        preserving its attributes
sortByChromAndStart     Sorting 'GRanges-class' objects
str2chr                 String to Character
str2dig                 String to Digits
translation             Translation of DNA/RNA sequences
