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CLI Tools

DNALLM provides a comprehensive set of command-line interface tools for various DNA language model tasks.

Available Commands

Core Commands

  • dnallm train - Fine-tune DNA language models
  • dnallm inference - Run inference with trained models
  • dnallm benchmark - Compare multiple models
  • dnallm mutagenesis - Perform in silico mutagenesis

Server Commands

  • dnallm mcp-server - Start MCP (Model Context Protocol) server
  • dnallm-mcp-server - Standalone MCP server script

Configuration Tools

  • dnallm model-config-generator - Interactive configuration file generator

Quick Start

# Generate a configuration file
dnallm model-config-generator --output finetune_config.yaml

# Train a model
dnallm train --config finetune_config.yaml

# Run inference
dnallm inference --config inference_config.yaml --model-path ./models/trained_model

# Benchmark models
dnallm benchmark --config benchmark_config.yaml

# Start MCP server
dnallm mcp-server --config mcp_server_config.yaml

Configuration

All DNALLM commands use YAML configuration files that define:

  • Task parameters (classification, regression, generation, etc.)
  • Model settings and hyperparameters
  • Data preprocessing options
  • Evaluation metrics and output formats

Getting Help

# Show help for a specific command
dnallm train --help

# Show general help
dnallm --help

Next Steps