treeflow.evolution.substitution.probabilities module

treeflow.evolution.substitution.probabilities.get_transition_probabilities_eigen(eigen: Eigendecomposition, t: Tensor) → Tensor

Get transition probabilities for an eigendecomposition of a rate matrix and a time (i.e. genetic distances in expected substitutions per site).

Parameters:

• eigen – Eigendecomposition of Tensors (can have batch dimensions)

• t – Time Tensor (can be batched)

Returns:

Transition probabilities with shape […, state, state] where … is batch shape

Return type:

Tensor

treeflow.evolution.substitution.probabilities.get_batch_transition_probabilities_eigen(eigen: Eigendecomposition, t: Tensor, batch_rank: int = 1, inner_batch_rank: int = 0) → Tensor

Get transition probabilities for an eigendecomposition of a rate matrix and a time (i.e. genetic distances in expected substitutions per site).

Parameters:

• eigen – Eigendecomposition of Tensors (can have batch dimensions …)

• t – Tensor of times with shape (…, branches)

Returns:

Transition probabilities with shape (…, branches)

Return type:

Tensor

treeflow.evolution.substitution.probabilities.get_transition_probabilities_tree(tree: TensorflowUnrootedTree, subst_model: SubstitutionModel, rate_categories: Tensor | None = None, batch_rank: int = 0, inner_batch_rank: int = 0, **subst_params) → TensorflowUnrootedTree