What is the key difference between Atlas and DeepDNA?

Atlas belongs to the Developer Tools category with local stdio execution, while DeepDNA belongs to the Developer Tools category with local stdio execution.

How do I install Atlas or DeepDNA in Claude Desktop or Cursor?

Copy the mcpServers JSON configuration snippet provided on this page into your claude_desktop_config.json or ~/.cursor/mcp.json file and restart your AI client.

Are Atlas and DeepDNA free or paid?

Atlas operates under a Free / Open Source model (No auth required). DeepDNA operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Atlas lists 0 tools with 2 views and 1 GitHub stars. DeepDNA lists 0 tools with 0 views and 0 GitHub stars.

Can I use both Atlas and DeepDNA together in the same MCP host?

Yes! MCP hosts like Claude Desktop, Cursor, Windsurf, Cline, and VS Code support configuring multiple servers under the mcpServers object simultaneously.

Side-by-Side Model Context Protocol Comparison

Atlas vs DeepDNA

In-depth architectural comparison of the Atlas and DeepDNA MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

At a Glance & Executive Verdict

Atlas

Developer Tools · Local stdio

Quality: 44/100 (Fair) | Auth: No auth required

DeepDNA

Developer Tools · Local stdio

Quality: 25/100 (Emerging) | Auth: No auth required

Verdict Summary: Choose Atlas if you need specialized Developer Tools tools running via a local process. Choose DeepDNA if your workspace requires Developer Tools integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.

Which MCP Server Should You Choose?

Choose Atlas when:

You need dedicated capabilities in the Developer Tools domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).

Explore Atlas Details

Choose DeepDNA when:

You need dedicated capabilities in the Developer Tools domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).

Explore DeepDNA Details

Feature & Specification Comparison

Specification	Atlas Developer Tools	D DeepDNA Developer Tools
Summary	Atlas is a YAML-defined semantic layer for analytics — authored by humans, consumed by AI agents.	Cited gene, variant (rsID) and CPIC drug–gene lookups for AI agents. Read-only, no key.
Category & Scope	Developer Tools	Developer Tools
Quality signal

Tools & Capabilities Breakdown

Atlas Tools (0)

No explicit tool names declared in metadata yet. Check project README on main listing page.

DeepDNA Tools (0)

No explicit tool names declared in metadata yet. Check project README on main listing page.

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

Atlas Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "atlas-2": {
      "command": "bunx",
      "args": [
        "@useatlas/mcp"
      ]
    }
  }
}

DeepDNA Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "deepdna": {
      "command": "npx",
      "args": [
        "-y",
        "deepdna"
      ]
    }
  }
}

Frequently Asked Questions

Atlas is categorized under Developer Tools and uses a local stdio subprocess. In contrast, DeepDNA belongs to Developer Tools using local stdio subprocess. Select Atlas when you need capabilities focused on developer tools and DeepDNA when you require tools for developer tools.

More alternatives to Atlas More alternatives to DeepDNA Developer Tools category hub