The PyPI distribution is dnadesign-tools; Python imports remain dnadesign.
dnadesign is a modular bioinformatics toolkit for designing sequence libraries, assembling DNA constructs, running sequence models, and analyzing the resulting datasets.
Documentation
Use the docs index to choose a workflow, inspect existing work, or jump to a tool.
- Docs index: main index for workflow, tool, and repository docs.
- Installation: bootstrap the environment and run baseline verification commands.
- Architecture, Design, Reliability, Security, Plans, Quality score: repository-level contracts and governance records.
- Developer docs: CI contracts, maintenance runbooks, and execution-planning references.
Available tools
Pick the tool that matches the work you need to do. Each link opens the tool README for commands, inputs, and outputs.
Design, modeling, and analysis
| Tool | Description |
|---|---|
| usr | Store, check, and sync tables of sequence records. |
| densegen | Generate DNA sequence libraries from saved design inputs. |
| infer | Run sequence models and add their predictions to datasets. |
| construct | Build DNA constructs from reusable templates. |
| junction | Turn exact DNA targets into checked three-way-junction oligo plans. |
| opal | Use measured results to choose which DNA designs to test next. |
| cluster | Group similar rows and visualize the groups. |
| latentdna | Compare sequence features and save tables and plots for review. |
| cruncher | Design DNA sequences and assembly plans within stated limits. |
| billboard | Measure how much binding-site content varies across a sequence library. |
| libshuffle | Choose smaller, representative sets from large sequence libraries. |
| nmf | Find motif patterns that repeatedly occur together in a data table. |
| permuter | Create sequence variants and evaluate them with selected tools. |
| tfkdanalysis | Summarize experiments that reduce selected transcription factors. |
| aligner | Compare pairs or sets of DNA and protein sequences. |
| thread | Prepare protein-design jobs and check the predicted structures. |
Draw and inspect results
| Tool | Description |
|---|---|
| folding | Predict and draw how RNA sequences fold. |
| baserender | Draw annotated sequence maps from saved jobs. |
Run and monitor jobs
| Tool | Description |
|---|---|
| ops | Find, run, and inspect jobs across dnadesign. |
| notify | Send notifications for local and scheduled jobs. |
Data shared between tools
| Tool | Description |
|---|---|
| contracts | Define versioned file formats shared between tools. |
1 maintainer
Metadata
1 maintainer
Release files for dnadesign-tools 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| dnadesign_tools-0.2.0.tar.gz | 5.4 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| dnadesign_tools-0.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 12.7 MB
Release files / dnadesign_tools-0.2.0.tar.gz
| Download URL | dnadesign_tools-0.2.0.tar.gz |
|---|---|
| Size | 5.4 MB |
| Tags | Source |
|
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Transparency logRelease files / dnadesign_tools-0.2.0-py3-none-any.whl
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| Size | 7.3 MB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
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PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 7, 2026.
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