albert-ying/.autolab/acquired_skills/orthofinder
.autolab/acquired_skills/orthofinder/SKILL.md
# OrthoFinder Skill ## When to Use Use OrthoFinder for identifying orthologous gene groups across multiple genomes, inferring gene trees, and identifying orthogroups (clusters of orthologous genes). ## Standard Workflow 1. Prepare protein FASTA files (one per genome) from gene predictions 2. Run OrthoFinder: `orthofinder -f <protein_fasta_dir>` 3. Parse results from Orthogroups/Orthogroups.tsv 4. Filter orthogroups present in all species (core orthogroups) ## Key Decisions - Use protein seque
$ install --global
skillsauthnpx skillsauth add albert-ying/autonomous-lab .autolab/acquired_skills/orthofinderInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
OrthoFinder Skill
When to Use
Use OrthoFinder for identifying orthologous gene groups across multiple genomes, inferring gene trees, and identifying orthogroups (clusters of orthologous genes).
Standard Workflow
- Prepare protein FASTA files (one per genome) from gene predictions
- Run OrthoFinder:
orthofinder -f <protein_fasta_dir> - Parse results from Orthogroups/Orthogroups.tsv
- Filter orthogroups present in all species (core orthogroups)
Key Decisions
- Use protein sequences (not nucleotide) for ortholog detection
- Choose appropriate inflation parameter for MCL clustering
- Filter single-copy orthologs for phylogenetic analysis
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