Synthetic Biology Python Packages

dna-features-viewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

dnachisel

:pencil2: A versatile DNA sequence optimizer

snapgene-reader

👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.

gen

Git for genomes

dnacauldron

:alembic: Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies

codontransformer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

factorforge-cds

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

sequenticon

:space_invader: Generate identicons for DNA sequences with Python

ostir

Software for predicting translation initiation rates in bacteria

ypkpathway

Automatic pathway assembly with the YeastPathwayKit

streptocad

StreptoCAD is an open-source toolbox that automates the design of genome engineering strategies in Streptomyces. It supports CRISPR-based workflows, generating primers, guide sequences, and plasmid simulations to accelerate genetic engineering and natural product discovery.

geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

deepbgc

BGC Detection and Classification Using Deep Learning

ggassembler

Design Golden Gate assemblies in the Yeast Toolkit (YTK) standard. Local desktop-in-browser app: detection by digest, never by annotation.

tatapov

:paw_prints: DNA overhang misannealing data for Python

dnaweaver

A route planner for DNA assembly

symbac

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

evolutionary-stability-optimizer

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

genome-collector

:stars: Easily download genomes and build BLAST/Bowtie indexes in Python

dnadesign

A lua package for designing DNA.

strider-dna

A Python library for nucleic acid thermodynamics, kinetics, and DNA/RNA circuit design with end-to-end simulation pipelines.

teemi

teemi: A Python package for reproducible and FAIR microbial strain construction. Simulate the entire dbtl-cycle, generate genetic parts, design libraries, and track samples. Open-source Python platform for workflow flexibility and automated tasks, accelerating metabolic engineering. Try teemi with our Google Colab notebooks!

bandwagon

🎺 Plot DNA digestion band patterns with Python

goldenhinges

:link: Short overhangs design for DNA assembly