bio-alignment-io
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, a…
Maintainer Lylll9436 · Last updated April 1, 2026
Systematic top-down workflow for polishing academic papers. Structure to logic to expression with user confirmation at each step.
Original source
https://github.com/Lylll9436/Paper-Polish-Workflow-skill/tree/main/skills/paper-polish-workflow
Skill Snapshot
Source Doc
| File | Purpose |
|---|---|
references/expression-patterns.md | Academic expression patterns overview and module index |
| File | When to Load |
|---|---|
references/expression-patterns/introduction-and-gap.md | Polishing introduction or background content |
references/expression-patterns/methods-and-data.md | Polishing methods, data, or study area content |
references/expression-patterns/results-and-discussion.md | Polishing results or discussion content |
references/expression-patterns/conclusions-and-claims.md | Polishing conclusion content |
references/expression-patterns/geography-domain.md | Content involves spatial, urban, or planning topics |
references/anti-ai-patterns.md | Polishing expression (Step 3) -- screen for AI-sounding phrases |
references/journals/ceus.md | Target journal is CEUS |
Before starting, ask about:
Rules:
direct mode, skip pre-questions if the user provided enough context.batch mode, skip per-item questions; apply settings from the first item.skill-conventions.md > AskUserQuestion Enforcement for full rules.Related skills
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, a…
Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical s…
Generate or optimize academic paper abstracts using the 5-sentence Farquhar formula. Supports generate-from-scratch and restructure-existing…
Generate or optimize figure/table captions for academic papers. Geography-aware: study area, CRS notation, data source. Writes output to.tex…