# Md5fa

> Use when hashing FASTA records and comparing ordered versus order-insensitive sequence digests instead of taking a single whole-file MD5.

- Skill: `vimalinx/md5fa` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add vimalinx/md5fa`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/md5fa/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-08-19
- Page: https://skillmd.com/skills/vimalinx/md5fa

---


# md5fa

md5fa is an HTSlib-based FASTA digester. It emits one MD5 per FASTA record plus two aggregate summaries, `>ordered` and `>unordered`, so it is materially different from `md5sum` on the raw file bytes.

## Quick Start

- **Command:** `md5fa <fasta>`
- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/md5fa`
- **Live output shape:** `md5  fasta_path  record_label`

## When To Use This Tool

- Hash FASTA content at the record level instead of hashing the literal file bytes.
- Compare two FASTA files while distinguishing "same records, different order" from "different sequence content".
- Generate stable per-sequence digests for reference or manifest workflows.

## Common Patterns

```bash
# 1) Hash every FASTA record plus aggregate ordered/unordered summaries
md5fa sample.fa
```

```bash
# 2) Use the >unordered line when record order should not matter
md5fa a.fa
md5fa b.fa
# in local testing, swapping record order changed >ordered but kept >unordered identical
```

```bash
# 3) Capture the digest table for later comparison
md5fa sample.fa > sample.fa.md5fa.txt
```

## Recommended Workflow

1. Run `md5fa` on a valid FASTA file rather than on arbitrary text.
2. Compare the per-record lines first if you need to identify which sequence changed.
3. Compare `>ordered` when record order is meaningful and `>unordered` when you only care about the multiset of records.
4. Store the full output table, not just one line, because the aggregate summaries capture different invariants.

## Guardrails

- `md5fa -h` is not help; it is treated as a filename and errors with `md5fa: -h: No such file or directory`.
- This is not a whole-file checksum tool. A multi-record FASTA produces one digest per record plus `>ordered` and `>unordered`.
- In live testing, swapping the order of two FASTA records changed the `>ordered` digest but left `>unordered` unchanged.
- An empty FASTA emitted the normal empty MD5 for `>ordered` (`d41d8cd98f00b204e9800998ecf8427e`) and an all-zero digest for `>unordered`.
- Output includes three fields: digest, source FASTA path, and record label. Downstream parsers should not assume a plain two-column `md5sum` layout.