Key Conclusion
The 4 tools in the graph comparison (semantica, trustgraph, mempalace, neural-memory) are NOT good choices for source code indexing.
Among the 14 repos, graphify, code-review-graph, and gitnexus are the three that specialize in source code. graphify parses 23 languages with tree-sitter, keeps a persistent graph, and lists a 71.5× token reduction. code-review-graph covers 19 languages plus Jupyter, stores the index in SQLite, and focuses on blast radius. gitnexus is the zero-server option, with LadybugDB and a browser UI. The other four are built for documents or general memory, not for code indexing.
These tools focus on:
- semantica: Document-based KG, reasoning, audit trail
- trustgraph: Multi-model data, enterprise knowledge
- mempalace: Memory system, Palace structure
- neural-memory: Graph-based memory, spreading activation
Best Tools for Source Code Indexing
Among the 14 repos, 3 tools specialize in source code:
graphify ⭐ Best
| Feature | Support |
|---|---|
| Languages | 23 languages (Python, JS, TS, Go, Rust, Java, C++, etc.) |
| AST Parsing | ✅ tree-sitter |
| Code Indexing | ✅ Persistent graph (graph.json) |
| Code Search | ✅ query, path, explain commands |
| Token Reduction | 71.5× |
| MCP | ✅ (MCP server) |
| Output | graph.html (interactive), GRAPH_REPORT.md |
How it works:
- AST pass - deterministic extraction (classes, functions, imports, call graphs)
- Semantic pass - Claude extracts concepts, relationships, design rationale
- Output: NetworkX graph + Leiden community detection
code-review-graph
| Feature | Support |
|---|---|
| Languages | 19 languages + Jupyter |
| AST Parsing | ✅ tree-sitter |
| Code Indexing | ✅ SQLite |
| Code Search | ✅ Blast-radius, impact analysis |
| Token Reduction | 8.2× - 49× |
| MCP | ✅ (22 tools) |
| Output | D3.js visualization |
Strengths:
- Incremental updates (<2s)
- 100% recall on impact analysis
- Auto-update on file edit/git commit
gitnexus
| Feature | Support |
|---|---|
| Languages | Multiple (tree-sitter based) |
| AST Parsing | ✅ tree-sitter |
| Code Indexing | ✅ LadybugDB |
| Code Search | ✅ MCP tools (query, context, impact) |
| MCP | ✅ (16 tools) |
| Architecture | Zero-server (WASM) |
Strengths:
- Runs in browser (WASM)
- Zero-server architecture
- Enterprise features (PR review, wiki)
Detailed Comparison
| Feature | graphify | code-review-graph | gitnexus | semantica | trustgraph | mempalace | neural-memory |
|---|---|---|---|---|---|---|---|
| Languages | 23 | 19+ | Multiple | Generic | Generic | ❌ | ❌ |
| AST Parsing | ✅ tree-sitter | ✅ tree-sitter | ✅ tree-sitter | ⚠️ basic | ❌ | ❌ | ❌ |
| Code Indexing | ✅ | ✅ | ✅ | ❌ | ❌ | ❌ | ❌ |
| Code Search | ✅ | ✅ | ✅ | ❌ | ❌ | ❌ | ❌ |
| Token Reduction | 71.5× | 8.2-49× | - | - | - | - | - |
| MCP | ✅ | ✅ (22) | ✅ (16) | ❌ | ✅ | ✅ | ✅ (56) |
| Offline | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
Recommendations
For Source Code Indexing & Searching
| Use Case | Recommendation | Reason |
|---|---|---|
| Codebase understanding | graphify | 71.5× token reduction, 23 languages, AST parsing |
| Code review | code-review-graph | Blast-radius, impact analysis |
| Code intelligence | gitnexus | Zero-server, WASM, enterprise |
| Simple code search | code-review-graph | Fast, incremental updates |
Not Recommended for Source Code
| Tool | Reason |
|---|---|
| semantica | Document-focused, no AST parsing |
| trustgraph | Enterprise knowledge, not code analysis |
| mempalace | Memory system, no code features |
| neural-memory | Memory library, not focused on code |
Quick Decision
What do you need?
│
├─► Index & Search Source Code
│ ├─► Token optimization (71.5×) → graphify
│ ├─► Code review, impact analysis → code-review-graph
│ ├─► Zero-server, WASM → gitnexus
│ ├─► Speed + auto-sync, MIT → codegraph
│ ├─► Most languages, zero-dependency → codebase-memory-mcp
│ └─► Graph + git history + code health + decisions → repowise
│
├─► Knowledge Graph / Semantic Search (documents)
│ ├─► Audit, reasoning → semantica
│ ├─► Multi-model enterprise → trustgraph
│ └─► Memory system → mempalace / neural-memory
│
└─► Vector Search Only
└─► zvec (high-performance)
Conclusion: To index and search a project's source code, use graphify (best for token reduction), code-review-graph (for review), gitnexus (for enterprise, accepting its noncommercial license), codegraph (fastest, auto-sync, pure MIT), codebase-memory-mcp (most languages, zero-dependency), or repowise (if you need git analytics/code health/decisions and not just a graph).
September 2026 Update — 3 New Tools (repowise, codegraph, codebase-memory-mcp)
These three tools were not in the original comparison table (04/2026) because they appeared or became popular afterward. See each tool's details: Repowise, CodeGraph, Codebase Memory MCP.
| Tool | Core language | Languages parsed | MCP tools | License | Differentiator |
|---|---|---|---|---|---|
| repowise | Python | 26 | 10 (task-shaped) | AGPL-3.0/commercial | Graph + git analytics + code health + ADR mining, PR bot |
| codegraph | Rust kernel | 20 | focused on codegraph_explore |
MIT | Fastest, auto-sync via OS file watcher, self-scales to the machine |
| codebase-memory-mcp | Pure C | 162 | 15 | MIT | Zero-dependency (single binary), Hybrid LSP, makes no network calls itself |
A note on trustworthiness: all three (and gitnexus as well) are very young (created 08/2025–03/2026) yet have reached 6.7k–71.5k GitHub stars — the ratio of watchers/followers to stars is lower than typical for long-established popular repos. This is not evidence of fraud, but you should verify further (commit history, community discussion) and avoid piping curl | bash/curl | sh straight into a shell where possible, before fully trusting the self-published benchmark numbers/badges in a README.
An AST pass extracts classes, functions, imports, and call graphs. A semantic pass asks Claude for concepts, relationships, and design rationale. code-review-graph updates in under 2 seconds and states 100% recall on impact analysis, with 22 MCP tools and a token cut between 8.2× and 49×. repowise parses 26 languages and adds git analytics, code health, and ADR mining under AGPL-3.0. codegraph is a Rust kernel with an OS file watcher and an MIT license. codebase-memory-mcp is a single C binary that parses 162 languages and makes no network calls itself.
Updated: 2026-04-13, supplemented 2026-09-20
See also: Graph Comparison · Memory Tool Comparison · Graphify