treeflow.traversal.phylo_likelihood module
- treeflow.traversal.phylo_likelihood.move_indices_to_outside(x, start, size)
- treeflow.traversal.phylo_likelihood.phylogenetic_likelihood(sequences_onehot: Tensor, transition_probs: Tensor, frequencies: Tensor, postorder_node_indices: Tensor, child_indices: Tensor, batch_shape=())
Per-site phylogenetic likelihood. Assumes all parameters are broadcastable w.r.t. batch shape
- sequences_onehot
Tensor with shape […, leaf, state]
- transition_probs
Tensor with shape […, node, state, state] Must be broadcasted over sites
- frequencies
Tensor with shape […, state]
- postorder_node_indices
Tensor with shape [internal_node]. Cannot have batch dimensions.
- child_indices
Tensor with shape [internal_node, children]