# Rust build artifacts
target/
Cargo.lock

# Python virtual environments and caches
venv/
__pycache__/
*.pyc
*.pyo
*.pyd
.Python
env/
*.egg-info/
.venv/

# Miscellaneous
*.log
*.tmp
*.phy
*.swp
*.vcf
*.bed
*.png
*.pdf
.DS_Store
web/figures-site/public/downloads/supplementary_tables.xlsx

# Node/Next.js artifacts
node_modules/
**/node_modules/
.next/
**/.next/
out/
**/out/
web/figures-site/.turbo/
per_site_diversity_output.falsta
per_site_fst_output.falsta
iqtree-3.0.1-Linux/
paml/
pipeline_run_*.log
region_trees/
tree_figures/
annotated_tree_figures/
