ClaudSkills / Science & Research / biology-medicine

Bio Comparative Genomics Whole Genome Alignment

Q: What is a Claude Code skill and how does the Bio Comparative Genomics Whole Genome Alignment skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Bio Comparative Genomics Whole Genome Alignment is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Science & Research · Sub-category: biology-medicine · Last updated: 2026-06-02

Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

About this skill (catalog notes)

Bio Comparative Genomics Whole Genome Alignment includes 5 code blocks for direct copy-paste. At roughly 4,095 words the SKILL.md is on the longer end of the catalog distribution.

Source: bg-szy.github.io/TOP-SKILLS
Original author: bg-szy
Indexed lastmod: 2026-06-02
Catalog position: Science & Research · biology-medicine
Indexed related skills: 10

How Bio Comparative Genomics Whole Genome Alignment fits the catalog

Bio Comparative Genomics Whole Genome Alignment sits in the Science & Research category under the biology-medicine sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.

These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.

What this skill does

Bio Comparative Genomics Whole Genome Alignment is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-comparative-genomics-whole-genome-alignment/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

Who uses this skill

The Bio Comparative Genomics Whole Genome Alignment Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 93,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/bio-comparative-genomics-whole-genome-alignment
curl -L https://claudskills.com/skills/bio-comparative-genomics-whole-genome-alignment/SKILL.md \
  -o ~/.claude/skills/bio-comparative-genomics-whole-genome-alignment/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-comparative-genomics-whole-genome-alignment/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/bio-comparative-genomics-whole-genome-alignment/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-comparative-genomics-whole-genome-alignment\SKILL.md on Windows. See the full install guide for step-by-step instructions.

📱 Install from your phone or desktop Telegram

Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.

Pro

For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.

See pricing → Download desktop app

Frequently asked questions

How do I install the Bio Comparative Genomics Whole Genome Alignment Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/bio-comparative-genomics-whole-genome-alignment/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the Bio Comparative Genomics Whole Genome Alignment skill do?

Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

When should I use the Bio Comparative Genomics Whole Genome Alignment skill?

Use Bio Comparative Genomics Whole Genome Alignment when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Bio Comparative Genomics Whole Genome Alignment" or describe the task and let Claude pick). Browse related skills at /category/science/.

What is a Claude Code skill and how does the Bio Comparative Genomics Whole Genome Alignment skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Bio Comparative Genomics Whole Genome Alignment is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/bg-szy/TOP-SKILLS/blob/HEAD/skills/awesome-skills/bio-comparative-genomics-whole-genome-alignment/SKILL.md
Author: bg-szy
Website: https://bg-szy.github.io/TOP-SKILLS/

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA

bg-szy. (2026). Bio Comparative Genomics Whole Genome Alignment [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-comparative-genomics-whole-genome-alignment/

BibTeX

@misc{bio-comparative-genomics-whole-genome-alignment-2026,
  author    = {bg-szy},
  title     = {Bio Comparative Genomics Whole Genome Alignment [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/bio-comparative-genomics-whole-genome-alignment/}
}

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