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"Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "autm_3d" ] }, { "page": "autm_z125", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "autm_z125" ] }, { "page": "automorphism_bycoef", "title": "Automorphism Grouping by Coefficient", "topics": [ "automorphism_bycoef", "automorphism_bycoef,Automorphism-method", "automorphism_bycoef,AutomorphismList-method" ] }, { "page": "automorphism_prob", "title": "Automorphism Probability", "topics": [ "automorphism_prob", "automorphism_prob,AutomorphismByCoef-method", "automorphism_prob,AutomorphismByCoefList-method" ] }, { "page": "automorphismByRanges", "title": "Get the automorphisms by ranges.", "topics": [ "automorphismByRanges", "automorphismByRanges,Automorphism-method", "automorphismByRanges,AutomorphismList-method" ] }, { "page": "automorphisms", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.", "topics": [ "automorphisms", "automorphisms,DNAMultipleAlignment-method", "automorphisms,DNAStringSet_OR_NULL-method" ] }, { "page": "autZ125", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in \\mathbb{Z}_{125}.", "topics": [ "autZ125" ] }, { "page": "autZ5", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in \\mathbb{Z}_5.", "topics": [ "autZ5" ] }, { "page": "autZ64", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in \\mathbb{Z}_{64}.", "topics": [ "autZ64" ] }, { "page": "base_methods", "title": "DNA Sequences Methods", "topics": [ "base_coord", "base_coord,DNAMultipleAlignment-method", "base_coord,DNAStringSet_OR_NULL-method", "base_matrix", "base_matrix,DNAMultipleAlignment-method", "base_matrix,DNAStringSet_OR_NULL-method", "base_methods", "base_seq2string_set", "base_seq2string_set,BaseSeq-method", "seq2granges", "seq2granges,DNAMultipleAlignment-method", "seq2granges,DNAStringSet_OR_NULL-method" ] }, { "page": "base2codon", "title": "Split a DNA sequence into codons", "topics": [ "base2codon", "base2codon,character-method", "base2codon,DNAMultipleAlignment-method", "base2codon,DNAStringSet-method" ] }, { "page": "base2int", "title": "Replace bases with integers from \\mathbb{Z}_4 and \\mathbb{Z}_5", "topics": [ "base2int", "base2int,character-method", "base2int,data.frame-method" ] }, { "page": "brca1_aln", "title": "Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.", "topics": [ "brca1_aln" ] }, { "page": "brca1_aln2", "title": "Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.", "topics": [ "brca1_aln2" ] }, { "page": "brca1_autm", "title": "Automorphisms between DNA Sequences from Primate BRCA1 Genes", "topics": [ "brca1_autm" ] }, { "page": "brca1_autm2", "title": "Automorphisms between DNA Sequences from Primate BRCA1 Genes", "topics": [ "brca1_autm2" ] }, { "page": "cdm_z64", "title": "Codon Distance Matrices for the Standard Genetic Code on \\mathbb{Z}_4", "topics": [ "cdm_z64" ] }, { "page": "codon_coord", "title": "Codon coordinates on a given Abelian group representation.", "topics": [ "codon_coord", "codon_coord,BaseGroup-method", "codon_coord,DNAMultipleAlignment-method", "codon_coord,DNAStringSet_OR_NULL-method", "codon_coord,matrix_OR_data_frame-method" ] }, { "page": "codon_dist", "title": "Weighted Manhattan Distance Between Codons", "topics": [ "codon_dist", "codon_dist,character-method", "codon_dist,CodonGroup_OR_Automorphisms-method", "codon_dist,DNAStringSet-method" ] }, { "page": "codon_dist_matrix", "title": "Compute Codon Distance Matrix", "topics": [ "codon_dist_matrix" ] }, { "page": "codon_matrix", "title": "Codon Coordinate Matrix", "topics": [ "codon_matrix", "codon_matrix,BaseSeqMatrix-method", "codon_matrix,DNAMultipleAlignment-method", "codon_matrix,DNAStringSet-method" ] }, { "page": "conserved_regions", "title": "Conserved and Non-conserved Regions from an MSA", "topics": [ "conserved_regions", "conserved_regions,Automorphism-method", "conserved_regions,AutomorphismByCoef-method", "conserved_regions,AutomorphismByCoefList-method", "conserved_regions,AutomorphismList-method" ] }, { "page": "covid_aln", "title": "Pairwise Sequence Alignment (MSA) of COVID-19 genomes.", "topics": [ "covid_aln" ] }, { "page": "covid_autm", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "covid_autm" ] }, { "page": "cyc_aln", "title": "Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C", "topics": [ "cyc_aln" ] }, { "page": "cyc_autm", "title": "Automorphisms between DNA Sequences from Primate Cytochrome C Genes", "topics": [ "cyc_autm" ] }, { "page": "dna_phyche", "title": "Some Physicochemical Properties of DNA bases", "topics": [ "dna_phyche" ] }, { "page": "dna_phychem", "title": "DNA numerical matrix", "topics": [ "dna_phychem", 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Abelian Group", "topics": [ "matrices", "matrices,CodonSeq-method", "matrices,DNAMultipleAlignment-method", "matrices,DNAStringSet_OR_NULL-method", "matrices,MatrixList-method" ] }, { "page": "mod", "title": "Modulo Operation", "topics": [ "'%%'", "mod", "mod,matrix,numeric-method", "modulo" ] }, { "page": "modlineq", "title": "Modular System of Linear Equation Solver (MLE)", "topics": [ "modlineq" ] }, { "page": "mut_type", "title": "Classification of DNA base mutations", "topics": [ "mut_type" ] }, { "page": "peptide_phychem_index", "title": "Amino acid numerical matrix", "topics": [ "peptide_phychem_index", "peptide_phychem_index,character-method", "peptide_phychem_index,DNAStringSet_OR_DNAMultipleAlignment-method" ] }, { "page": "seqranges", "title": "Get DNA sequence Ranges and Coordinates representation on a given Abelian Group", "topics": [ "seqranges", "seqranges,CodonSeq-method", "seqranges,DNAMultipleAlignment-method", "seqranges,DNAStringSet_OR_NULL-method" ] }, { "page": 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