Manual

This manual provides comprehensive guides for using PhyloZoo. For exact specifics of each function and class, see the API Reference.

Contents:

• Introduction
  • What is PhyloZoo?
  • Package Structure
  • Design Philosophy
  • Getting Started
• Installation
  • Installing PhyloZoo
    • Requirements
  • Verifying Installation
  • Building Documentation
  • Troubleshooting
• Core Module
  • Overview
    • Submodules
    • See Also
  • Multiple Sequence Alignments
    • Working with Multiple Sequence Alignments
    • Bootstrap Resampling
    • Distance Computation
    • See Also
  • Pairwise Distances
    • Working with Distance Matrices
    • Classification Functions
    • Split Decomposition
    • See Also
  • Splits
    • Overview
    • Splits
    • Split Systems
  • Quartets
    • Overview
    • Quartets
    • Quartet Profiles
    • Quartet Profile Sets
  • Triplets
    • Overview
    • Triplets
    • Triplet Profiles
    • Triplet Profile Sets
  • Networks
    • Overview
    • Directed Networks
    • Semi-Directed Networks
  • Primitives
    • Overview
    • Partitions
    • Circular Orderings
    • Directed Multi-Graphs
    • Mixed Multi-Graphs
• Visualization Module
  • Overview
    • See Also
  • Plotting
    • How to Plot
    • Layouts
    • Saving a Figure
    • See Also
  • Styling
    • Using Styles
    • Styling Parameters
    • Example
    • See Also
• Utilities Module
  • Overview
    • Submodules
    • See Also
  • Input/Output (I/O)
    • Overview
    • I/O Operations
    • File Formats
    • Registering a New Format
  • Exceptions
    • Errors
    • Warnings
    • See Also
  • Validation
    • What is validation?
    • Which classes are validation-aware?
    • Disabling validation
    • Using the decorator for your own classes
    • See Also
  • Parallel Execution
    • How parallelization is organized
    • Configuring parallel execution
    • Using an executor directly
    • Pattern for PhyloZoo functions
    • See Also
• Bibliography