├── .gitpod.yml ├── .vscode └── settings.json ├── LICENSE ├── README.md ├── assets ├── icor-flat-banner.png ├── icor-flat-gear.svg ├── icor-flat-small.png ├── icor-full-visualization.png ├── icor-small-visualization.png └── icor-thin-gear.svg ├── benchmark_results ├── BFC_benchmarks.csv ├── ERC_benchmarks.csv ├── HFC_benchmarks.csv ├── URC_benchmarks.csv ├── genscript_benchmarks.csv ├── icor_benchmarks.csv └── original_benchmarks.csv ├── benchmark_sequences ├── BFC │ ├── AKT1_dna.fasta │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── EMG1_dna.fasta │ ├── FALVAC-1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── FLT1_dna.fasta │ ├── GSK3B_dna.fasta │ ├── HPDF_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LCK_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── MMPL3_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── NPR1_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PA_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PEA_dna.fasta │ ├── PIM1_dna.fasta │ ├── PLK1_dna.fasta │ ├── PTP4A3_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ ├── UBTF_dna.fasta │ └── pak1_dna.fasta ├── ERC │ ├── AKT1_dna.fasta │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── EMG1_dna.fasta │ ├── FALVAC-1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── FLT1_dna.fasta │ ├── GSK3B_dna.fasta │ ├── HPDF_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LCK_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── MMPL3_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── NPR1_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PAK1_dna.fasta │ ├── PA_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PEA_dna.fasta │ ├── PIM1_dna.fasta │ ├── PLK1_dna.fasta │ ├── PTP4A3_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ └── UBTF_dna.fasta ├── HFC │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── GSK3B_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PLK1_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ ├── akt1_dna.fasta │ ├── emg1_dna.fasta │ ├── falvac-1_dna.fasta │ ├── flt1_dna.fasta │ ├── hpdf_dna.fasta │ ├── lck_dna.fasta │ ├── mmpl3_dna.fasta │ ├── npr1_dna.fasta │ ├── pa_dna.fasta │ ├── pak1_dna.fasta │ ├── pea_dna.fasta │ ├── pim1_dna.fasta │ ├── ptp4a3_dna.fasta │ └── ubtf_dna.fasta ├── URC │ ├── AKT1_dna.fasta │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── EMG1_dna.fasta │ ├── FALVAC-1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── FLT1_dna.fasta │ ├── GSK3B_dna.fasta │ ├── HPDF_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LCK_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── MMPL3_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── NPR1_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PA_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PEA_dna.fasta │ ├── PIM1_dna.fasta │ ├── PLK1_dna.fasta │ ├── PTP4A3_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ ├── UBTF_dna.fasta │ └── pak1_dna.fasta ├── aa │ ├── BIRC5_aa.fasta │ ├── BRAF1_aa.fasta │ ├── CAV1_aa.fasta │ ├── CD80_aa.fasta │ ├── CDK1_aa.fasta │ ├── CEBPZ_aa.fasta │ ├── CLN3_aa.fasta │ ├── CREB1_aa.fasta │ ├── CSNK1A1_aa.fasta │ ├── FGFR4_aa.fasta │ ├── GSK3B_aa.fasta │ ├── JUN_aa.fasta │ ├── KIF11_aa.fasta │ ├── LAMP1_aa.fasta │ ├── LEMD3_aa.fasta │ ├── MAPK1_aa.fasta │ ├── MAPKAPK5_aa.fasta │ ├── NGFR_aa.fasta │ ├── NOC2L_aa.fasta │ ├── OPRM1_aa.fasta │ ├── PDCD11_aa.fasta │ ├── PLK1_aa.fasta │ ├── RPS6KB1_aa.fasta │ ├── SMARCD1_aa.fasta │ ├── TAP1_aa.fasta │ ├── TAS2R10_aa.fasta │ ├── akt1_aa.fasta │ ├── emg1_aa.fasta │ ├── falvac-1_aa.fasta │ ├── flt1_aa.fasta │ ├── hpdf_aa.fasta │ ├── lck_aa.fasta │ ├── mmpl3_aa.fasta │ ├── npr1_aa.fasta │ ├── pa_aa.fasta │ ├── pak1_aa.fasta │ ├── pea_aa.fasta │ ├── pim1_aa.fasta │ ├── ptp4a3_aa.fasta │ └── ubtf_aa.fasta ├── all_original │ ├── allFastaAA.fasta │ └── allFastaDNA.fasta ├── dna │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── GSK3B_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PLK1_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ ├── akt1_dna.fasta │ ├── emg1_dna.fasta │ ├── falvac-1_dna.fasta │ ├── flt1_dna.fasta │ ├── hpdf_dna.fasta │ ├── lck_dna.fasta │ ├── mmpl3_dna.fasta │ ├── npr1_dna.fasta │ ├── pa_dna.fasta │ ├── pak1_dna.fasta │ ├── pea_dna.fasta │ ├── pim1_dna.fasta │ ├── ptp4a3_dna.fasta │ └── ubtf_dna.fasta ├── genscript │ ├── AKT1_dna.fasta │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── EMG1_dna.fasta │ ├── FALVAC-1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── FLT1_dna.fasta │ ├── GSK3B_dna.fasta │ ├── HPDF_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LCK_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── MMPL3_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── NPR1_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PA_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PEA_dna.fasta │ ├── PIM1_dna.fasta │ ├── PLK1_dna.fasta │ ├── PTP4A3_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ ├── UBTF_dna.fasta │ └── pak1_dna.fasta └── icor │ ├── BIRC5_dna.fasta │ ├── BRAF1_dna.fasta │ ├── CAV1_dna.fasta │ ├── CD80_dna.fasta │ ├── CDK1_dna.fasta │ ├── CEBPZ_dna.fasta │ ├── CLN3_dna.fasta │ ├── CREB1_dna.fasta │ ├── CSNK1A1_dna.fasta │ ├── FGFR4_dna.fasta │ ├── GSK3B_dna.fasta │ ├── JUN_dna.fasta │ ├── KIF11_dna.fasta │ ├── LAMP1_dna.fasta │ ├── LEMD3_dna.fasta │ ├── MAPK1_dna.fasta │ ├── MAPKAPK5_dna.fasta │ ├── NGFR_dna.fasta │ ├── NOC2L_dna.fasta │ ├── OPRM1_dna.fasta │ ├── PDCD11_dna.fasta │ ├── PLK1_dna.fasta │ ├── RPS6KB1_dna.fasta │ ├── SMARCD1_dna.fasta │ ├── TAP1_dna.fasta │ ├── TAS2R10_dna.fasta │ ├── akt1_dna.fasta │ ├── emg1_dna.fasta │ ├── falvac-1_dna.fasta │ ├── flt1_dna.fasta │ ├── hpdf_dna.fasta │ ├── lck_dna.fasta │ ├── mmpl3_dna.fasta │ ├── npr1_dna.fasta │ ├── pa_dna.fasta │ ├── pak1_dna.fasta │ ├── pea_dna.fasta │ ├── pim1_dna.fasta │ ├── ptp4a3_dna.fasta │ └── ubtf_dna.fasta ├── requirements.txt ├── tool ├── models │ └── icor.onnx ├── optimizers │ ├── BFC_optimizer.py │ ├── ERC_optimizer.py │ ├── HFC_optimizer.py │ ├── URC_optimizer.py │ └── icor_optimizer.py ├── resources │ ├── Benchmarking Results & Comparison - ICOR Codon Optimization.pdf │ ├── codon_map.xlsx │ └── ecoli_codon_frequencies.csv └── scripts │ ├── convert_to_cds.ipynb │ ├── csv_to_seqs.py │ ├── reformat_seqs.py │ └── run_benchmark.ipynb 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