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skills/phylo_from_buscos/README.md

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+# BUSCO-based Phylogenomics Skill
+
+A Claude Code skills for phylogenomic analyses, created by Bruno de Medeiros (Field Museum) based on code initially written by Paul Frandsen (Brigham Young University)
+
+It generate a complete phylogenetic workflow from genome assemblies using BUSCO/compleasm-based single-copy orthologs.
+
+**Features:**
+- Supports local genome files and NCBI accessions (BioProjects/Assemblies)
+- Generates scheduler-specific scripts (SLURM, PBS, cloud, local)
+- Uses modern tools (compleasm, MAFFT, IQ-TREE, ASTRAL)
+- Multiple alignment trimming options
+- Both concatenation and coalescent approaches
+- Quality control with recommendations
+- Writes a draft methods paragraph describing the pipeline for publications
+
+**Use when you need to:**
+- Build phylogenetic trees from multiple genome assemblies
+- Extract and align single-copy orthologs across genomes
+- Download genomes from NCBI by accession
+- Generate ready-to-run scripts for your computing environment
+
+## Installation
+See README on the repository root folder for plugin installation.
+
+
+## Usage
+
+Once installed, simply describe your phylogenomics task:
+
+```
+I need to generate a phylogeny from 20 genome assemblies on a SLURM cluster
+```
+
+Claude Code will automatically activate the appropriate skill and guide you through the workflow.
+
+## Workflow Overview
+
+The complete phylogenomics pipeline:
+
+1. **Input Preparation** - Download NCBI genomes if needed
+2. **Ortholog Identification** - Run compleasm/BUSCO on all genomes
+3. **Quality Control** - Assess genome completeness with recommendations
+4. **Ortholog Extraction** - Generate per-locus unaligned FASTA files
+5. **Alignment** - Align orthologs with MAFFT
+6. **Trimming** - Remove poorly aligned regions (Aliscore/ALICUT, trimAl, BMGE, ClipKit)
+7. **Concatenation** - Build supermatrix with partition scheme
+8. **Phylogenetic Inference** - Generate ML concatenated tree (IQ-TREE), gene trees, and coalescent species tree (ASTRAL)
+
+## Requirements
+
+Claude Code is better than the web interface, since Claude will then help you install all requirements.
+
+The skill generates scripts that install and use:
+
+- **compleasm** or BUSCO - ortholog detection
+- **MAFFT** - multiple sequence alignment
+- **Aliscore/ALICUT, trimAl, BMGE, or ClipKit** - alignment trimming
+- **FASconCAT** - alignment concatenation
+- **IQ-TREE** - maximum likelihood phylogenetic inference
+- **ASTRAL** - coalescent species tree estimation
+- **NCBI Datasets CLI** - genome download (if using NCBI accessions)
+
+
+## Computing Environments
+
+The skill supports multiple computing environments:
+
+- **SLURM clusters** - generates SBATCH array jobs
+- **PBS/Torque clusters** - generates PBS array jobs
+- **Local machines** - sequential execution scripts
+
+## Attribution
+
+Created by **Bruno de Medeiros** (Curator of Pollinating Insects, Field Museum) based on phylogenomics tutorials by **Paul Frandsen** (Brigham Young University).
+
+## Citation
+
+If you use this skill for published research, please cite this website and also:
+
+- **compleasm**: Huang, N., & Li, H. (2023). compleasm: a faster and more accurate reimplementation of BUSCO. *Bioinformatics*, 39(10), btad595.
+- **MAFFT**: Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7. *Molecular Biology and Evolution*, 30(4), 772-780.
+- **IQ-TREE**: Minh, B. Q., et al. (2020). IQ-TREE 2: New models and efficient methods for phylogenetic inference. *Molecular Biology and Evolution*, 37(5), 1530-1534.
+- **ASTRAL**: Zhang, C., et al. (2018). ASTRAL-III: polynomial time species tree reconstruction. *BMC Bioinformatics*, 19(6), 153.
+
+Plus any trimming tool you use (Aliscore/ALICUT, trimAl, BMGE, or ClipKit).
+
+## License
+
+MIT License - see individual tool licenses for software dependencies.
+
+## Support
+
+For issues or questions:
+- Open an issue in this repository
+- Contact Bruno de Medeiros at the Field Museum (bdemedeiros@fieldmuseum.org)
+
+## Acknowledgments
+
+Special thanks to Paul Frandsen (BYU) for creating the excellent phylogenomics tutorials that form the foundation of this skill.