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BytesAgain β€Ί Skills β€Ί Protein Phylogeny
πŸ¦€ ClawHub

Protein Phylogeny

by @billwanttobetop

Comprehensive protein family phylogenetic analysis workflow with quality control, conservation analysis, coevolution network analysis, and publication-ready...

Versionv1.5.0
#crypto#can-make-purchases#clawhub
πŸ’‘ Examples

Input: FASTA file with protein sequences (any family, any size) Output: Publication-ready report with phylogenetic tree, conservation analysis, coevolution networks, and high-quality figures

Typical workflow: 

# 1. Quality control (removes low-quality sequences)
bash scripts/01_quality_control.sh input.fasta output_dir/
2. Conservation analysis

bash scripts/02_conservation.sh output_dir/qc/final.fasta output_dir/
3. Coevolution analysis

bash scripts/03_coevolution.sh output_dir/qc/final.fasta output_dir/
4. Phylogenetic tree

bash scripts/04_phylogeny.sh output_dir/qc/final.fasta output_dir/
5. Generate figures

bash scripts/05_visualize.sh output_dir/
6. Create report

bash scripts/06_report.sh output_dir/ "Family Name"

πŸ“‹ Tips & Best Practices

Issue: CD-HIT crashes with large datasets Fix: Split input, process in batches, merge results

Issue: IQ-TREE runs forever Fix: Use -fast mode or reduce bootstrap replicates

Issue: Figures look pixelated Fix: Increase DPI in scripts/05_visualize.sh (default 300)

Issue: Report generation fails Fix: Check all intermediate files exist, rerun failed stages

View on ClawHub
TERMINAL
clawhub install protein-phylogeny

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