Overview

The phylozoo.core.primitives module provides fundamental data structures that serve as building blocks for phylogenetic analysis in PhyloZoo. These classes represent core mathematical concepts used throughout the library, including partitions, circular orderings, and graph primitives that form the foundation for network-based phylogenetics.

Some classes on this page can be imported from the core primitives module:

from phylozoo.core.primitives import *
# or directly
from phylozoo.core.primitives import (
    Partition,
    CircularOrdering,
    CircularSetOrdering,
)

Graph classes and functions are imported from their submodules:

from phylozoo.core.primitives.d_multigraph import DirectedMultiGraph
from phylozoo.core.primitives.m_multigraph import MixedMultiGraph

Submodules

• Partition - Set partitions and refinement relationships

• Circular Ordering - Circular arrangements of elements and sets

• Directed Multi-Graph - Directed graphs with parallel edges

• Mixed Multi-Graph - Mixed graphs with both directed and undirected edges

See Also

• API Reference - Complete function signatures and detailed examples

• Networks - Network classes that use these primitives

• Splits - Split systems based on partitions