treeflow.model package

class treeflow.model.PhyloModel(model_dict: Dict[str, str | Dict[str, object]])

Bases: object

Class to represent the configuration of a basic phylogenetic model

classmethod check_model_dict(model_dict: Dict[str, str | Dict[str, object]])
all_params() → Dict[str, object]
free_params() → Dict[str, Dict[str, object]]
relaxed_clock() → bool
treeflow.model.phylo_model_to_joint_distribution(model: PhyloModel, initial_tree: TensorflowRootedTree, initial_alignment: Alignment, pattern_counts: Tensor | None = None, use_native: str | bool = 'auto', unroll: str | bool = 'auto', include_likelihood: bool = True) → JointDistributionCoroutine

Build the joint distribution for a phylogenetic model.

Parameters:

  • use_native – Forwarded to the sequence likelihood (LeafCTMC) to select the native C++ tree-likelihood op (True), the pure-TensorFlow implementation (False), or automatic selection ("auto").

  • include_likelihood – When False the sequence (alignment) likelihood term is omitted, so the resulting distribution is the prior over all latent parameters. This is useful for profiling the prior and likelihood contributions to the target density separately.

Subpackages

Submodules