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| sscu-package | Strength of Selected Codon Usage |
| akashi_test | akashi test for codon usage |
| genomic_gc3 | genomic gc3 for an multifasta genomic file |
| optimal_codons | Identify optimal codons by using the highly expressed genes method |
| optimal_codons_table | statistical table for the optimal codons |
| optimal_codon_statistics | statistical table for the optimal codons |
| op_corre_CodonW | Identify optimal codons by using the correlative method from Hershberg & Petrov, the input file is from CodonW |
| op_corre_NCprime | Identify optimal codons by using the correlative method from Hershberg & Petrov, the input file is from NCprime |
| op_highly | Identify optimal codons by using the highly expressed genes method |
| proportion_index | optimal codons index for the four and six codon boxes |
| selected_codons | Identify optimal codons by using the highly expressed genes method |
| s_index | S index (Strength of Selected Codon Usage) |