albert-ying/autonomous-lab/orthofinder
Claude Code and agent skill by albert-ying/autonomous-lab
Trust tier 3
- community
Source check pending
Checking that the SKILL.md file is still in the repository.
Install
npx vskill@latest install albert-ying/autonomous-lab/orthofinderSKILL.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
Security
- Security scanPassed, 90 of 100Pattern checks on the skill's files.
- Model reviewPassed
Quality evaluation
- Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
Source
- SKILL.md in the repositoryChecking.autolab/acquired_skills/orthofinder/SKILL.md
Popularity
- 7-day trend score
- 5
Not refreshed yet.
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