PhyNetPy API Reference

Welcome to the PhyNetPy documentation. PhyNetPy is a comprehensive Python library for phylogenetic network analysis, providing tools for network construction, manipulation, simulation, and inference.

Module Index

Module	Description
Alphabet	Character-to-state mapping for biological sequence data (DNA, RNA, Protein, Codon, SNP).
BiMarkers	SNP (biallelic marker) likelihood computation for phylogenetic networks, with optional GPU acceleration.
BirthDeath	Birth-death process network simulators (Yule and CBDP models).
Executor	Computation backend abstraction layer providing CPU (NumPy) and GPU (CuPy) array operations.
GTR	Time-reversible nucleotide substitution models (GTR, JC, K80, F81, HKY, K81, SYM, TN93).
GeneTrees	Gene tree container and analysis utilities including consensus tree construction and concordance factors.
GraphUtils	Graph and network utility functions for topology analysis, manipulation, and ASCII rendering.
IO	Central I/O hub for reading and writing phylogenetic file formats (FASTA, VCF, Newick, Nexus).
Logger	Simple debug logger for internal model move compatibility.
MSA	Multiple Sequence Alignment parsing, storage, grouping, and distance computation.
Matrix	Data matrix storage and reduction for sequence alignments with unique site pattern compression.
MetropolisHastings	Metropolis-Hastings MCMC and Hill Climbing search algorithms for phylogenetic inference.
ModelFactory	Component-based model building factory for constructing probabilistic phylogenetic models.
ModelGraph	Probabilistic graphical model for phylogenetics with typed model nodes and visitor pattern support.
ModelMove	Network topology move operations for MCMC search (add/remove/flip reticulation, SPR).
Network	Core phylogenetic network data structures: Node, Edge, and Network classes.
NetworkMoves	Network topology modification operations for MCMC search (add/remove hybrid, NNI, node height).
Newick	Newick format label extraction and Nexus file generation utilities.
Phylo	Core Branch class for storing phylogenetic edge attributes (length, inheritance probability).
PhyloNet	PhyloNet Java wrapper for running external phylogenetic analysis tools.
SNPSimulator	SNP data simulator for phylogenetic networks using a forward-in-time 2-state CTMC.
State	State management for MCMC accept/reject decisions with model validation.
Strategy	Strategy pattern interface for node-level computations dispatched during bottom-up traversal.
Traversal	Iterator-based graph traversal for model nodes supporting pre-order, post-order, and level-order.
Validation	Comprehensive file format validation for phylogenetic data files (Newick, Nexus, FASTA, PHYLIP, etc.).
Visitor	Visitor pattern interface for ModelNode traversals with typed dispatch.
graph_core	Graph core data structures with automatic Cython acceleration for NodeSet and EdgeSet.

Getting Started

Installation

pip install phynetpy

Quick Example

from PhyNetPy import Network, Node, Edge
from PhyNetPy import read_nexus, read_newick

# Parse a network from a Nexus file
networks = read_nexus("my_network.nex")
network = networks[0]

# Access network properties
print(f"Number of nodes: {len(network.V())}")
print(f"Number of edges: {len(network.E())}")
print(f"Leaves: {[leaf.label for leaf in network.get_leaves()]}")

# Parse from a Newick string
net = read_newick("((A:0.1,B:0.2):0.3,C:0.4);")

# Simulate a network
from PhyNetPy import CBDP
sim = CBDP(gamma=1.0, mu=0.5, n=10)
simulated_net = sim.generate_network()

Module Categories

Core Data Structures

• Alphabet - Character-to-state mapping for biological sequence data (DNA, RNA, Protein, Codon, SNP).
• MSA - Multiple Sequence Alignment parsing, storage, grouping, and distance computation.
• Matrix - Data matrix storage and reduction for sequence alignments with unique site pattern compression.
• Network - Core phylogenetic network data structures: Node, Edge, and Network classes.
• Phylo - Core Branch class for storing phylogenetic edge attributes (length, inheritance probability).

Models

• GTR - Time-reversible nucleotide substitution models (GTR, JC, K80, F81, HKY, K81, SYM, TN93).

Simulation

• BirthDeath - Birth-death process network simulators (Yule and CBDP models).
• SNPSimulator - SNP data simulator for phylogenetic networks using a forward-in-time 2-state CTMC.

Inference

• BiMarkers - SNP (biallelic marker) likelihood computation for phylogenetic networks, with optional GPU acceleration.
• MetropolisHastings - Metropolis-Hastings MCMC and Hill Climbing search algorithms for phylogenetic inference.
• ModelMove - Network topology move operations for MCMC search (add/remove/flip reticulation, SPR).
• NetworkMoves - Network topology modification operations for MCMC search (add/remove hybrid, NNI, node height).
• State - State management for MCMC accept/reject decisions with model validation.

Analysis

• GeneTrees - Gene tree container and analysis utilities including consensus tree construction and concordance factors.
• GraphUtils - Graph and network utility functions for topology analysis, manipulation, and ASCII rendering.

I/O

• IO - Central I/O hub for reading and writing phylogenetic file formats (FASTA, VCF, Newick, Nexus).
• Newick - Newick format label extraction and Nexus file generation utilities.
• PhyloNet - PhyloNet Java wrapper for running external phylogenetic analysis tools.
• Validation - Comprehensive file format validation for phylogenetic data files (Newick, Nexus, FASTA, PHYLIP, etc.).

Infrastructure

• Executor - Computation backend abstraction layer providing CPU (NumPy) and GPU (CuPy) array operations.
• Logger - Simple debug logger for internal model move compatibility.
• ModelFactory - Component-based model building factory for constructing probabilistic phylogenetic models.
• ModelGraph - Probabilistic graphical model for phylogenetics with typed model nodes and visitor pattern support.
• Strategy - Strategy pattern interface for node-level computations dispatched during bottom-up traversal.
• Traversal - Iterator-based graph traversal for model nodes supporting pre-order, post-order, and level-order.
• Visitor - Visitor pattern interface for ModelNode traversals with typed dispatch.
• graph_core - Graph core data structures with automatic Cython acceleration for NodeSet and EdgeSet.