Bio Comparative Genomics Gene Tree Species Tree Reconciliation

Q: What is a Claude Code skill and how does the Bio Comparative Genomics Gene Tree Species Tree Reconciliation 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 Gene Tree Species Tree Reconciliation is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the General category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: General · Sub-category: general-misc · Last updated: 2026-06-02

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

About this skill (catalog notes)

Bio Comparative Genomics Gene Tree Species Tree Reconciliation includes pricing or quota commentary; 7 code blocks for direct copy-paste. At roughly 4,432 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: General · general-misc
Indexed related skills: 10

How Bio Comparative Genomics Gene Tree Species Tree Reconciliation fits the catalog

Bio Comparative Genomics Gene Tree Species Tree Reconciliation sits in the General category under the general-misc 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 Gene Tree Species Tree Reconciliation is a community-contributed Claude Code skill in the general-misc sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

Who uses this skill

The Bio Comparative Genomics Gene Tree Species Tree Reconciliation Claude Code skill is built for Claude Code users and developers across all disciplines looking for general-purpose AI assistance. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 119,000+ 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-gene-tree-species-tree-reconciliation
curl -L https://claudskills.com/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/SKILL.md \
  -o ~/.claude/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-comparative-genomics-gene-tree-species-tree-reconciliation\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 Gene Tree Species Tree Reconciliation 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-gene-tree-species-tree-reconciliation/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the Bio Comparative Genomics Gene Tree Species Tree Reconciliation 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 Gene Tree Species Tree Reconciliation skill?

Use Bio Comparative Genomics Gene Tree Species Tree Reconciliation when your Claude Code task falls under the General category — specifically in the general misc 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 Gene Tree Species Tree Reconciliation" or describe the task and let Claude pick). Browse related skills at /category/general/.

What is a Claude Code skill and how does the Bio Comparative Genomics Gene Tree Species Tree Reconciliation 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 Gene Tree Species Tree Reconciliation is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the General 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-gene-tree-species-tree-reconciliation/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 Gene Tree Species Tree Reconciliation [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/

BibTeX

@misc{bio-comparative-genomics-gene-tree-species-tree-reconciliation-2026,
  author    = {bg-szy},
  title     = {Bio Comparative Genomics Gene Tree Species Tree Reconciliation [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/bio-comparative-genomics-gene-tree-species-tree-reconciliation/}
}

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