Getting Started

Requirements

• Python 3.10+

Installation

pip install factorforge-cds

For development:

git clone https://github.com/eijex/factorforge-cds.git
cd factorforge
pip install -e ".[dev]"

Docker (local web app)

Run the full web interface locally — no data leaves your machine:

docker pull ghcr.io/eijex/factorforge-cds:latest
docker run -p 8080:8080 ghcr.io/eijex/factorforge-cds:latest

Then open http://localhost:8080.

Sequence Length Limits

Mode	Max length	Notes
Web API (protein input)	5,000 aa	Vercel serverless timeout constraint
Web API (DNA/CDS input)	15,000 bp	≈ 5,000 aa
CLI / Docker	No limit	Local computation, install via pip install factorforge-cds

Quick Start

CLI:

factorforge optimize my_protein.fasta -o output.fasta

Python API:

from factorforge.engines.profile.pipeline import OptimizationPipeline

pipeline = OptimizationPipeline(profile="balanced")
result = pipeline.run("MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEG...")
print(result.sequence)   # optimized CDS
print(result.metadata)   # CAI, GC%, scan results, domestication edits

Eijex MCP

Use FactorForge from any MCP-compatible client:

{
  "mcpServers": {
    "eijex": {
      "type": "http",
      "url": "https://mcp.eijex.com/api/mcp"
    }
  }
}

Available tools:

Tool	Description
factorforge_cds_optimize	Optimize a single protein sequence
factorforge_cds_compare	Compare multiple profiles side-by-side
factorforge_cds_batch	Optimize up to 20 sequences at once

See mcp.eijex.com for the current public tool list.

Updating

pip:

pip install --upgrade factorforge-cds

Docker:

docker pull ghcr.io/eijex/factorforge-cds:latest

Git clone:

git pull origin main
pip install -e ".[dev]"

Check your installed version:

pip show factorforge-cds
# or
factorforge --version

Release notes: CHANGELOG