A side-by-side look at the Codetopo — code graph for AI agents and Repo Graph MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Codetopo — code graph for AI agents for biology & bioinformatics work; choose Repo Graph for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
orient, find, impact.Rows where the two servers differ are marked.
| Spec | C Codetopo — code graph for AI agents | |
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 36/100 · Fair | 63/100 · Good |
| Install command | Not confirmed yet | Confirmed |
| Transport | — | Local subprocess (stdio) |
| Auth | No auth required | No auth required |
| Pricing | Free | Free |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 1 | 58 |
| Directory activity | 0 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | Not listed | 6 |
| Full listing | View Codetopo — code graph for AI agents | View Repo Graph |
No tool names declared yet. Check the project README from the listing page.
orientGet the lay of the land — ALWAYS the first call on a codebase. With no arguments: a counts + entry-points overview plus a `blind spots` note flagging which (language, edge-kind) extractions are partial so you know where to fall back to grep. With `seed=<node>`: the dense structural map scoped to that node's neighbourhood. With `full=true`: the whole-repo dense map (the full context dump). Orient first, then `find` to jump to nodes, `impact` for blast radius, `trace` for flows.findTurn any text into the ranked nodes that matter — the on-ramp to the graph. A symbol or keyword returns matching nodes; a pasted stacktrace / failing-test id / diff is resolved to the code it implicates and ranked by relevance. Set `expand=true` to fan out to the surrounding neighbourhood (spreading activation). Every row carries `path:line`, so `read` the top hits directly — no grep.impactBlast radius in one call: fan out from one or more nodes to everything they affect (forward) or depend on / are used by (backward), returned as a complete, deduped, Personalized-PageRank-ranked, located closure. Each row carries `path:line`, the edge `via` reason it's in scope, and a `⊘` when the engine finds it unreachable from any entry point (likely dead). Structural import/containment fan-out is excluded — no noise. Depth-1 in both directions is a node's immediate neighbours. Pass several comma-separated nodes to assess a whole diff at once.traceFollow the code across boundaries. One argument: trace a feature end-to-end — the ordered path from entry through the stack, each hop labelled with its mechanism (call / HTTP / queue / event / data), crossing service boundaries (frontend→backend). Two arguments: the shortest path between two specific nodes, hop by hop. This is where the graph beats reading many files — it knows the cross-stack links grep can't see.readReturn the source code for one or more nodes, sliced from their files by the graph's line spans. Use after `find`/`impact` to read the exact code without grepping — comma-separate several node names to read the whole ranked set in a single call. Each node is a code block headed by its qname and `path:start-end`, plus a `context:` footer with structural facts the source alone doesn't show: HTTP method, cross-stack callers, covering tests, and intent/decision/constraint cells when present.refresh(Re)build the structural graph with tree-sitter AST parsing across 20 languages, running the cross-stack resolvers (HTTP, gRPC, GraphQL, WebSocket, queues, events, CLI). Incremental by default — only changed files re-parse — so it's cheap to call after edits; set `full=true` to force a clean reparse. Accepts a local path or a git URL (cloned on demand). Call after a major refactor; routine edits are picked up automatically by the file watcher.Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
No confirmed install command for Codetopo — code graph for AI agents yet — follow the setup steps linked from its listing page rather than a guessed package name.
{
"mcpServers": {
"james-chahwan-repo-graph": {
"command": "uvx",
"args": [
"mcp-repo-graph"
]
}
}
}