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Proto
Programmable biology: a constraint-based optimization language with 120+ bioinformatics tools
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- llms.txt
- https://proto.evodesign.org/docs/llms.txt
- llms-full.txt
- https://proto.evodesign.org/docs/llms-full.txt
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- 2023-07-04
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Their llms.txt
The beginning of the file, from our validated copy saved 2026-10-26T14:40:38.069Z. Cached copy · Source on evodesign.org
# Proto
> Programmable biology: a constraint-based optimization language with 120+ bioinformatics tools
- [Proto](https://proto.evodesign.org/docs/introduction.md): A high-level programming language for designing DNA, RNA, and protein sequences
- [Updates](https://proto.evodesign.org/docs/updates.md): Releases, events, and collaborations across the Proto project
- [Change Log](https://proto.evodesign.org/docs/changelog.md): New tools and recent development across the Proto language and tools layers
- [Introduction](https://proto.evodesign.org/docs/language/introduction.md): A constraint-based optimization framework for designing DNA, RNA, and protein sequences
- [Installation](https://proto.evodesign.org/docs/language/installation.md): Setting up Proto on CPU or GPU
- [Quickstart](https://proto.evodesign.org/docs/language/quickstart.md): Designing a biological sequence with constraint-based optimization
- [Architecture Overview](https://proto.evodesign.org/docs/language/concepts/overview.md): How Proto turns biological requirements into optimized sequences
- [Sequences](https://proto.evodesign.org/docs/language/concepts/sequences.md): The fundamental data unit for biological sequence representation
- [Segments](https://proto.evodesign.org/docs/language/concepts/segments.md): Defining sequence regions and managing dual pools during optimization
- [Constructs](https://proto.evodesign.org/docs/language/concepts/constructs.md): Combining segments into complete biological designs
- [Generators](https://proto.evodesign.org/docs/language/concepts/generators.md): Components that propose candidate sequences during optimization
- [Constraints](https://proto.evodesign.org/docs/language/concepts/constraints.md): Scoring functions that encode design requirements as values the optimizer minimizes
- [Optimizers](https://proto.evodesign.org/docs/language/concepts/optimizers.md): Search algorithms that find optimal biological sequences through iterative generate-score-select cycles
- [Programs](https://proto.evodesign.org/docs/language/concepts/programs.md): Chains multiple optimizers into a multi-stage pipeline for biological sequence design
- [Tools](https://proto.evodesign.org/docs/language/concepts/tools.md): Bioinformatics tools that Proto orchestrates for sequence analysis, structure prediction, and more
- [Using Constraints](https://proto.evodesign.org/docs/language/guides/using-constraints.md): Quantify design requirements with built-in and custom constraint functions
- [Using Generators](https://proto.evodesign.org/docs/language/guides/using-generators.md): Propose candidate sequences with built-in and custom generators across the mutation, autoregressive, inverse-folding, and gradient families
- [Using Optimizers](https://proto.evodesign.org/docs/language/guides/using-optimizers.md): Run the built-in optimizers and chain them into multi-stage searches over biological sequences
- [DNA Sequence Optimization](https://proto.evodesign.org/docs/language/gui
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