codon-optimization 开源项目推荐（38 个）

Edinburgh-Genome-Foundry /DnaChisel

✏️ A versatile DNA sequence optimizer

Adibvafa /CodonTransformer

CodonTransformer（2M+下载）;密码子优化工具，优化DNA以实现蛋白质表达

Lattice-Automation /icor-codon-optimization

RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8

Edinburgh-Genome-Foundry /python_codon_tables

📊 Codon usage tables in code-friendly format + Python bindings

Koeng101 /dnadesign

A lua package for designing DNA.

elementalcollision /GraphMemory-IDE

AI-assisted development MCP providing long-term, on-device "AI memory" for IDEs. Powered by Kuzu GraphDB and exposed via MCP server

lareaulab /Trias

Trias: an encoder-decoder model for generating synthetic eukaryotic mRNA sequences

RJain12 /choformer

Cho codon optimization WIP

tdseher /simple-codon-optimizer

Simple Python program to perform codon optimization or heterology calculations.

Maximato /Codonopt

Codonopt program is designed for codon optimization of protein sequences. The core of it based on the mathematical codon optimization proposed by Şen et al. (2020)

Boehringer-Ingelheim /SynCodonLM

Codon language model disentangled from protein level semantics.

poseidonchan /CodonTranslator

a decoder-only codon language model for codon optimization across all domains of life

eijex /factorforge-cds

Open-source CDS design and pre-synthesis sequence review for plant gene constructs.

anchitaaghag /Codon-Optimization-for-Biopharming

A tool to translate a given protein sequence into a DNA sequence based on a constructed codon use table for a target heterologous host, Nicotiana benthamiana.

Dr-Logvinovich /codon-torus-syntax

Open-source verification suite & preprints on Medium-Range Conditional Codon Syntax (54 RefSeq taxa, 10 null models H0-H7) & the Double-Stranded Codon Torus T_4^3 = (Z/4Z)^3: Markov lumpability, antisense channel dominance (74-88%), TP53/RAS intron-exon splicing, JCVI-syn1.0/3.0, BNT162b2/mRNA-1273 duplex forensics & Duplex-Safe Viterbi compiler.

HallemLab /Wild_Worm_Codon_Adapter

Shiny Web app for automatic codon optimization based on codon usage in Strongyloides species, Pristionchus species, Brugia malayi, as well as user-provided custom codon lookup tables

Gumgo91 /CodonHumanization

A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm

stracquadaniolab /cubseq-nf

CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.

Jarryd-W-Hoffman /vaccine-codon-optimiser

A lightweight, research-focused tool for optimising virus codons to improve compatibility with a target mRNA vaccine, with rule-based amino-acid-preserving transformations and built-in sequence comparisons.

xiongQvQ /codon-recoder

Recode a DNA sequence to match a target amino‑acid sequence with the minimal number of nucleotide changes, preserving the reading frame. Includes a CLI and Python API.