# Compute the automorphisms between DNA's Abelian group representations

## Documentation for package ‘GenomAutomorphism’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

'%%' | Modulo Operation
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
aa_index | Amino acid mutation matrix
aa_mutmat | Amino acid mutation matrix
aa_phychem_index | Amino acid mutation matrix
aln | Simulated 'DNAStringSet' class object
aminoacid_dist | Distance Between Aminoacids in Terms of Codon Distance
aminoacid_dist-method | Distance Between Aminoacids in Terms of Codon Distance
as.AutomorphismList | Methods for AutomorphismList-class Objects
as.AutomorphismList-method | 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
automorphismByRanges | Get the automorphisms by ranges.
automorphismByRanges-method | Get the automorphisms by ranges.
automorphisms | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.
automorphisms-method | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.
automorphism_bycoef | Autmorphism Grouping by Coefficient
automorphism_bycoef-method | Autmorphism Grouping by Coefficient
automorphism_prob | Autmorphism Probability
automorphism_prob-method | Autmorphism Probability
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.
base2codon | Split a DNA sequence into codons
base2codon-method | Split a DNA sequence into codons
base2int | Replace bases with integers from Z4 and Z5
base2int-method | Replace bases with integers from Z4 and Z5
base_coord | DNA Sequences Methods
base_coord-method | DNA Sequences Methods
base_matrix | DNA Sequences Methods
base_matrix-method | DNA Sequences Methods
base_methods | DNA Sequences Methods
base_seq2string_set | DNA Sequences Methods
base_seq2string_set-method | DNA Sequences Methods
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_coord-method | Codon coordinates on a given a given Abelian group representation.
codon_dist | Weighted Manhattan Distance Between Codons
codon_dist-method | Weighted Manhattan Distance Between Codons
codon_dist_matrix | Compute Codon Distance Matrix
codon_matrix | Codon Coordinate Matrix
codon_matrix-method | Codon Coordinate Matrix
conserved_regions | Conserved and Non-conserved Regions from a MSA
conserved_regions-method | 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
dna_phychem-method | DNA numerical matrix
getAutomorphisms | Get Automorphisms
getAutomorphisms-method | Get Automorphisms
get_coord | DNA base/codon sequence and coordinates represented on a given Abelian group.
get_coord-method | 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
get_mutscore-method | Get Mutation Score from an AAindex or a Mutation/Distance Matrix
matrices | Get the Coordinate Representation from DNA Sequences on Specified Abelian Group
matrices-method | Get the Coordinate Representation from DNA Sequences on Specified Abelian Group
mod | Modulo Operation
mod-method | Modulo Operation
modlineq | Modular System of Linear Equation Solver (MLE)
modulo | Modulo Operation
mut_type | Classification of DNA base mutations
peptide_phychem_index | Amino acid numerical matrix
peptide_phychem_index-method | Amino acid numerical matrix
seq2granges | DNA Sequences Methods
seq2granges-method | DNA Sequences Methods
seqranges | Get DNA sequence Ranges and Coordinates representation on a given Abelian Group
seqranges-method | Get DNA sequence Ranges and Coordinates representation on a given Abelian Group
slapply | Apply a function over a list-like object preserving its attributes
sortByChromAndEnd | Sorting 'GRanges-class' objects
sortByChromAndStart | Sorting 'GRanges-class' objects
str2chr | String to Character
str2chr-method | String to Character
str2dig | String to Digits
str2dig-method | String to Digits
translation | Translation of DNA/RNA sequences
translation-method | Translation of DNA/RNA sequences