API Reference

Complete API reference for all public functions, classes, and modules.

Core

Core data structures and classes for phylogenetic networks and related structures.

• core
  • network
    • dnetwork
    • sdnetwork
  • sequence
    • Main Class
    • Distance Computation
    • Bootstrap Functions
    • I/O Support
  • quartet
    • Main Classes
    • Distance Computation
  • split
    • Main Classes
    • Classification Functions
    • Algorithms
    • I/O Support
  • distance
    • Main Classes
    • Classification Functions
    • Operations
    • I/O Support
  • primitives
    • partition
    • circular_ordering
    • d_multigraph
    • m_multigraph

Visualization

Network visualization and plotting.

• viz
  • Plotting
    • plot()
  • Submodules
    • dnetwork
    • sdnetwork
    • d_multigraph
    • m_multigraph

Utilities

Utility functions and classes used throughout PhyloZoo.

• utils
  • io
    • IOMixin
    • File operations
    • FormatRegistry
    • Format utilities
  • exceptions
    • Base
    • General
    • Network
    • I/O
    • Algorithm
    • Visualization
    • Generator
    • Warnings
    • Warning utilities
  • validation
    • no_validation()
    • validation_aware()