dnadesign is a modular bioinformatics toolkit for designing sequence libraries, assembling DNA constructs, running sequence models, and analyzing the resulting datasets.
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.
Pick the tool that matches the work you need to do. Each link opens the tool README for commands, inputs, and outputs.
| 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. |
| msd | Resolve and compile typed Retron MSD designs. |
| 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. |
| Tool | Description |
|---|---|
| folding | Predict and draw how RNA sequences fold. |
| baserender | Draw annotated sequence maps from saved jobs. |
| Tool | Description |
|---|---|
| ops | Find, run, and inspect jobs across dnadesign. |
| notify | Send notifications for local and scheduled jobs. |
| Tool | Description |
|---|---|
| contracts | Define versioned file formats shared between tools. |