Payram Helper MCP Server vs Phylokit MCP

In-depth architectural comparison of the Payram Helper MCP Server and Phylokit 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 Payram Helper MCP Server 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 Payram Helper MCP Server Details

Choose Phylokit MCP 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 Phylokit MCP Details

Feature & Specification Comparison

Specification	Payram Helper MCP Server Developer Tools	Phylokit MCP Developer Tools
Summary	Remote MCP server to integrate and validate self-hosted Payram deployments.	Phylogenetic inference via IQ-TREE 2 — never returns a topology without its support
Category & Scope	Developer Tools	Developer Tools

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": {
    "payram-helper-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "skills"
      ]
    }
  }
}

{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ]
    }
  }
}

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