codon-optimization

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

A lua package for designing DNA.

Public MCP access to Eijex bioinformatics, literature lookup, and FactorForge CDS review tools.

Practical Python tools for the AI-leverage layers in mRNA cancer therapy. Stdlib-only: codon optimization, neoantigen screening, TrialGPT-style trial matching, and LNP composition advice.

SIRIUS is a synthetic biology tool that, given a peptide sequence, designs n maximally divergent gene sequences

Transcript-level red-flag scanner, expression predictor, and purification-strategy advisor for Chlamydomonas reinhardtii nuclear gene cassettes.

ESO - detects and removes hypermutable sites (recombination, slippage, methylation hotspots) from engineered DNA sequences while preserving translation and codon usage.

Codon language model disentangled from protein level semantics.

Codon Geometry Validation & Prediction Engine — algebraic structure of genetic codes in GF(2)^6

Exact synonymous codon optimization under GC, motif, homopolymer, and flank constraints

Clean-room Rust CLI for protein-faithful mRNA codon optimization research

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.

Phage library sequence generator with degenerate basepairs.

Codon optimization and structural modeling of perchlorate-reducing enzymes for Martian regolith bioremediation.

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

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

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

CpG-depleted, codon-optimised FST344 follistatin sequences for AAV gene therapy. AlphaFold3 validated.

✏️ A versatile DNA sequence optimizer

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.