Protein Family Phylogenetic Analysis

Complete workflow for protein family evolutionary analysis: quality control → conservation → coevolution → phylogeny → publication report.

Quick Start

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/