How do I install the Md5fa skill?

Run npx skillmds@latest add vimalinx/md5fa in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Md5fa safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Md5fa?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Md5fa free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Md5fa by vimalinx — Agent Skill

Name: Md5fa
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

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

# 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

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

Recommended Workflow

Run md5fa on a valid FASTA file rather than on arbitrary text.
Compare the per-record lines first if you need to identify which sequence changed.
Compare >ordered when record order is meaningful and >unordered when you only care about the multiset of records.
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.

---name: md5fadescription: Use when hashing FASTA records and comparing ordered versus order-insensitive sequence digests instead of taking a single whole-file MD5.---# md5famd5fa 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 summariesmd5fa sample.fa``````bash# 2) Use the >unordered line when record order should not mattermd5fa a.famd5fa b.fa# in local testing, swapping record order changed >ordered but kept >unordered identical``````bash# 3) Capture the digest table for later comparisonmd5fa sample.fa > sample.fa.md5fa.txt```## Recommended Workflow1. 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.

Frequently asked questions

Md5fa