# Optional dependencies for enhanced functionality

# Fast clustering
fastcluster>=1.2.0

# Tree operations and phylogenetic analysis
scikit-bio>=0.5.6

# Dynamic tree cutting (may need custom installation)
# dynamicTreeCut>=0.1.0

# Enhanced network analysis (may need custom installation)
# ensemble-networkx>=0.1.0

# Additional visualization and analysis
plotly>=5.0.0
dash>=2.0.0

# Development and testing
pytest>=6.0.0
pytest-cov>=2.10.0
black>=21.0.0
isort>=5.0.0
flake8>=3.8.0
mypy>=0.800

# Documentation
sphinx>=4.0.0
sphinx-rtd-theme>=0.5.0
nbsphinx>=0.8.0
myst-parser>=0.15.0

# Jupyter notebooks
jupyter>=1.0.0
ipykernel>=6.0.0
