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| codon_dist | Calculating the codon usage difference between sequences |
| codon_dist-method | Calculating the codon usage difference between sequences |
| codon_mimic | Mimic a target codon usage bias |
| codon_mimic-method | Mimic a target codon usage bias |
| codon_random | Generate random synonymous mutations |
| codon_random-method | Generate random synonymous mutations |
| codon_to | Maximize or minimize the usage of certain codon. |
| codon_to-method | Maximize or minimize the usage of certain codon. |
| dinu_dist | Calculating the dinucleotide usage difference between sequences |
| dinu_dist-method | Calculating the dinucleotide usage difference between sequences |
| dinu_to | Maximize or minimize the usage of certain dinucleotide. |
| dinu_to-method | Maximize or minimize the usage of certain dinucleotide. |
| get_cu | Get codon usage matrix |
| get_cu-method | Get codon usage matrix |
| get_dna | Get the DNAStringSet data |
| get_dna-method | Get the DNAStringSet data |
| get_du | Get dinucleotide usage matrix |
| get_du-method | Get dinucleotide usage matrix |
| get_freq | Get codon usage frequency of synonymous codons |
| get_freq-method | Get codon usage frequency of synonymous codons |
| get_nu | Get nucleotide usage matrix |
| get_nu-method | Get nucleotide usage matrix |
| get_region | Get the variable region |
| get_region-method | Get the variable region |
| get_rscu | Get Relative Synonymous Codon Usage (rscu) of synonymous codons |
| get_rscu-method | Get Relative Synonymous Codon Usage (rscu) of synonymous codons |
| input_seq | Import region / constructing regioned_dna object |
| input_seq-method | Import region / constructing regioned_dna object |
| regioned_dna-class | An S4 class to record DNA sequences and variable regions for mutations |
| seq_random | Generate 'n' random DNA sequnces of length 'm' |
| seq_random-method | Generate 'n' random DNA sequnces of length 'm' |