Mcp Code Indexer vs Clarity Mcp

In-depth architectural comparison of the Mcp Code Indexer and Clarity Mcp 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.

Which MCP Server Should You Choose?

Choose Mcp Code Indexer when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: Compiler-resolved code graph built with ts-morph, Reverse queries for callers, renderers, and references, Blast-radius, cycle, and orphan analysis.

Explore Mcp Code Indexer Details

Choose Clarity Mcp when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: check_ingredient, check_stack, find_alternatives.

Feature & Specification Comparison

Specification	Mcp Code Indexer Nishant-Chaudhary5338 Biology & Bioinformatics	Clarity Mcp thehealthai Biology & Bioinformatics
Summary	Index any TypeScript/React repo (including monorepos) into a queryable code graph. Reverse queries (who-renders, who-calls, find-references), blast-radius analysis, dependency cycles, dead-code orphans, and symbol signatures — exposed over stdio. Install: npx code-graph-indexer.	Condition-aware ingredient, product & supplement safety for agents, with provenance on every answer — a verdict, an evidence tier (Gold/Silver/Bronze), and a verifiable citation — across breastfeeding, pregnancy, histamine/MCAS, rosacea, HS, allergy and fertility lenses. 9 tools incl. validateclaim (fact-check a claim against curated cited sources) and checkrecall (FDA/consumer recall lookup by brand with Class I flagging and source URLs). Hosted at mcp.healthai.com.

Tools & Capabilities Breakdown

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).

{
  "mcpServers": {
    "nishant-chaudhary5338-mcp-code-indexer": {
      "command": "npx",
      "args": [
        "-y",
        "code-graph-indexer"
      ]
    }
  }
}

{
  "mcpServers": {
    "thehealthai-clarity-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "https://mcp.healthai.com"
      ]
    }
  }
}

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