> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.
# MSA Generator
> Sample mutations from MSA position-specific distributions
This generator is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.
Generator that samples mutations from MSA position-specific distributions.
This generator computes empirical probability distributions for each position
in a multiple sequence alignment, then mutates proposal sequences by sampling
from these distributions.
## API Reference
Configuration object for MSAGenerator.
This class defines configuration parameters for the MSA generator, which samples
mutations from position-specific probability distributions derived from a multiple
sequence alignment.
Multiple sequence alignment (list of aligned sequences).
Number of positions to mutate per sample
Whether to include gaps when calculating position probabilities
## Usage
```python python icon="python" theme={null}
>>> from proto_language.generator import MSAGenerator, MSAGeneratorConfig
>>> from proto_language.core import Segment
>>> from proto_tools.entities.msa import MSA
>>> config = MSAGeneratorConfig(
... msa=MSA(aligned_sequences=["MVLS", "AVLS", "MVLS"]),
... num_mutations=1,
... )
>>> gen = MSAGenerator(config)
>>> segment = Segment(sequence="MVLS", sequence_type="protein")
>>> gen.assign(segment)
>>> gen.sample() # Position 0 has 2/3 chance of M, 1/3 chance of A
```
## Metadata
| Property | Value |
| ------------------------ | ------------------- |
| Key | `msa` |
| Class | `MSAGenerator` |
| Category | `mutation` |
| Input Type | `starting_sequence` |
| Uses GPU | `False` |
| Supported Sequence Types | All |
| Allows Empty Start | `False` |
evo-design/proto-language/proto\_language/generator/msa\_generator.py
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