# Phylogeny Workflow

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- Skill: `jinze-lee/phylogeny-workflow` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add jinze-lee/phylogeny-workflow`
- Raw SKILL.md: https://api.skillmd.com/api/skills/jinze-lee/phylogeny-workflow/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Productivity
- Author: Jinze-Lee (https://skillmd.com/u/jinze-lee)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/jinze-lee/phylogeny-workflow

---

---
name: phylogeny-workflow
description: Follow the bundled phylogeny workflow. Use this skill only when the user explicitly invokes `$phylogeny-workflow`. Do not auto-select this skill for general phylogeny, tree plotting, or signal-analysis tasks.
---

# Phylogeny Workflow

## Overview

Use [references/source-note.md](references/source-note.md) as the source of truth for this skill.

Only use this skill when the user explicitly names `$phylogeny-workflow`.

Do not use this skill based on topic similarity alone.

## Workflow

1. Read [references/source-note.md](references/source-note.md) first.
2. Follow the note's tree-analysis workflow, output requirements, and styling expectations closely.
3. Replace stale input files, output folders, and intermediate processing steps with current project equivalents instead of copying blindly.
4. Preserve the original requirement that traceable data processing and figure generation should land in runnable R outputs.
5. If the note conflicts with the current user request, follow the current request and explain the adjustment.

## Source

- Bundled original note: `references/source-note.md`
- Installed skill name: `$phylogeny-workflow`