index.md

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

• Usage Guide - Complete CLI usage instructions and examples
• Configuration Generator - Learn how to create configuration files
• MCP Server - Learn about the Model Context Protocol server
• Fine-tuning Tutorials - Learn to train models
• Benchmark Tutorials - Compare model performance
• CLI Troubleshooting - Common CLI issues and solutions