Index

Symbols

--alignment-format treeflow_ml command line option treeflow_vi command line option --convergence-criterion treeflow_vi command line option --elbo-samples treeflow_vi command line option --init-values treeflow_ml command line option treeflow_vi command line option --input treeflow_ml command line option treeflow_vi command line option --learning-rate treeflow_ml command line option treeflow_vi command line option --model-file treeflow_ml command line option treeflow_vi command line option --n-output-samples treeflow_vi command line option --no-progress-bar treeflow_ml command line option treeflow_vi command line option --num-steps treeflow_ml command line option treeflow_vi command line option --optimizer treeflow_ml command line option treeflow_vi command line option --progress-bar treeflow_ml command line option treeflow_vi command line option --samples-output treeflow_vi command line option --seed treeflow_vi command line option --subnewick-format treeflow_ml command line option treeflow_vi command line option

--topology treeflow_ml command line option treeflow_vi command line option --trace-output treeflow_ml command line option treeflow_vi command line option --tree-output treeflow_ml command line option --tree-samples-output treeflow_vi command line option --variables-output treeflow_ml command line option --variational-approximation treeflow_vi command line option -c treeflow_vi command line option -i treeflow_ml command line option treeflow_vi command line option -m treeflow_ml command line option treeflow_vi command line option -n treeflow_ml command line option treeflow_vi command line option -o treeflow_ml command line option treeflow_vi command line option -r treeflow_ml command line option treeflow_vi command line option -s treeflow_vi command line option -t treeflow_ml command line option treeflow_vi command line option -va treeflow_vi command line option

A

AbstractRootedTree (class in treeflow.tree.rooted.base_rooted_tree) AbstractRootedTreeAttrs (class in treeflow.tree.rooted.base_rooted_tree) AbstractTree (class in treeflow.tree.base_tree) AbstractTreeTopology (class in treeflow.tree.topology.base_tree_topology) AbstractUnrootedTree (class in treeflow.tree.unrooted.base_unrooted_tree) add_inner_batch_dimensions() (treeflow.evolution.substitution.eigendecomposition.Eigendecomposition method) add_note() (treeflow.cli.inference_common.InitialValueParseError method) (treeflow.model.phylo_model.PhyloModelParseError method) add_to_tensor() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) adjoint() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) Alignment (class in treeflow) (class in treeflow.evolution) (class in treeflow.evolution.seqio) AlignmentFormat (class in treeflow) (class in treeflow.evolution) (class in treeflow.evolution.seqio) AlignmentType (class in treeflow) (class in treeflow.evolution) (class in treeflow.evolution.seqio) all_params() (treeflow.model.phylo_model.PhyloModel method) (treeflow.model.PhyloModel method) (treeflow.PhyloModel method) allow_nan_stats (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property)

anchor_heights (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector attribute) apply_gradients() (treeflow.vi.optimizers.robust_optimizer.RobustOptimizer method) args (treeflow.cli.inference_common.InitialValueParseError attribute) (treeflow.model.phylo_model.PhyloModelParseError attribute) assert_non_singular() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) assert_positive_definite() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) assert_self_adjoint() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) AttrsLengthMixin (class in treeflow.tf_util) (class in treeflow.tf_util.attrs)

B

BaseRootedTree (class in treeflow.tree.rooted.base_rooted_tree) BaseTreeDistribution (class in treeflow.distributions.tree.base_tree_distribution) BaseTreeTopology (class in treeflow.tree.topology.base_tree_topology) BaseUnrootedTree (class in treeflow.tree.unrooted.base_unrooted_tree) batch_shape (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) batch_shape_tensor() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method)

benchmark() (in module treeflow.cli.benchmark) bias_L (treeflow.bijectors.highway_flow.HighwayFlowParameters attribute) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained attribute) bias_U (treeflow.bijectors.highway_flow.HighwayFlowParameters attribute) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained attribute) bijectors (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) BirthDeathContemporarySampling (class in treeflow.distributions) (class in treeflow.distributions.tree) (class in treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling) bootstrap() (treeflow.debug.nonfinite_convergence_criterion.NonfiniteConvergenceCriterion method) (treeflow.vi.convergence_criteria.nonfinite.NonfiniteConvergenceCriterion method) branch_lengths (treeflow.tree.base_tree.AbstractTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs property) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree property) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree property) (treeflow.tree.unrooted.base_unrooted_tree.AbstractUnrootedTree attribute) (treeflow.tree.unrooted.base_unrooted_tree.BaseUnrootedTree attribute) (treeflow.tree.unrooted.numpy_unrooted_tree.NumpyUnrootedTree attribute) (treeflow.tree.unrooted.tensorflow_unrooted_tree.TensorflowUnrootedTree attribute) broadcast_structure() (in module treeflow.tf_util.vectorize) build_highway_L() (in module treeflow.model.approximation.cascading_flows) build_highway_lambd() (in module treeflow.model.approximation.cascading_flows) build_highway_U() (in module treeflow.model.approximation.cascading_flows) build_shift_and_scale_bijector() (in module treeflow.bijectors.highway_flow_node_bijector)

C

calculate_tree_stats() (in module treeflow.model.io) cdf() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) check_model_dict() (treeflow.model.phylo_model.PhyloModel class method) (treeflow.model.PhyloModel class method) (treeflow.PhyloModel class method) child_indices (treeflow.traversal.postorder.PostorderTopologyData attribute) (treeflow.tree.topology.base_tree_topology.AbstractTreeTopology property) (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology property) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology attribute) cholesky() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) clear() (treeflow.tree.taxon_set.DictTaxonSet method) components_distribution (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) cond() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) constant() (in module treeflow.model.phylo_model) constant_root_link() (in module treeflow.bijectors.highway_flow_node_bijector) ConstantCoalescent (class in treeflow.distributions.tree) (class in treeflow.distributions.tree.coalescent.constant_coalescent) convert_tree_to_tensor() (in module treeflow) (in module treeflow.tree) (in module treeflow.tree.rooted.tensorflow_rooted_tree) copy() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) (treeflow.tree.taxon_set.DictTaxonSet method)

count() (treeflow.tree.taxon_set.TupleTaxonSet method) (treeflow.vi.util.VIResults method) covariance() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) cross_entropy() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

D

DEFAULT_FLOAT_DTYPE_NP (in module treeflow.tf_util) (in module treeflow.tf_util.dtype_util) default_vi_trace_fn() (in module treeflow.vi.util) determinant() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) diag_part() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) DictTaxonSet (class in treeflow.tree.taxon_set) DiscreteParameterMixture (class in treeflow.distributions) (class in treeflow.distributions.discrete_parameter_mixture) DiscretizedDistribution (class in treeflow.distributions) (class in treeflow.distributions.discretized) distribution (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) domain_dimension (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) domain_dimension_tensor() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) dtype (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property)

E

eigen() (treeflow.evolution.substitution.base_substitution_model.EigendecompositionSubstitutionModel method) (treeflow.evolution.substitution.nucleotide.gtr.GTR method) (treeflow.evolution.substitution.nucleotide.hky.HKY method) (treeflow.evolution.substitution.nucleotide.jc.JC method) Eigendecomposition (class in treeflow.evolution.substitution.eigendecomposition) EigendecompositionSubstitutionModel (class in treeflow.evolution.substitution.base_substitution_model) eigenvalues (treeflow.evolution.substitution.eigendecomposition.Eigendecomposition attribute), [1] eigenvectors (treeflow.evolution.substitution.eigendecomposition.Eigendecomposition attribute), [1] eigvals() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) entropy() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) estimate_log_ml_importance_sampling() (in module treeflow.vi.marginal_likelihood) event_shape (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) event_shape_fn() (in module treeflow.model.event_shape_bijector) event_shape_tensor() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) experimental_batch_shape() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) experimental_batch_shape_tensor() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) experimental_compute_density_correction() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method)

experimental_default_event_space_bijector() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) experimental_fit() (treeflow.distributions.BirthDeathContemporarySampling class method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture class method) (treeflow.distributions.DiscreteParameterMixture class method) (treeflow.distributions.discretized.DiscretizedDistribution class method) (treeflow.distributions.DiscretizedDistribution class method) (treeflow.distributions.leaf_ctmc.LeafCTMC class method) (treeflow.distributions.LeafCTMC class method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain class method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain class method) (treeflow.distributions.sample_weighted.SampleWeighted class method) (treeflow.distributions.SampleWeighted class method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution class method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.birthdeath.yule.Yule class method) (treeflow.distributions.tree.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent class method) (treeflow.distributions.tree.ConstantCoalescent class method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution class method) (treeflow.distributions.tree.Yule class method) experimental_is_sharded (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) experimental_local_measure() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) experimental_sample_and_log_prob() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) experimental_shard_axis_names (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property)

F

FASTA (treeflow.AlignmentFormat attribute) (treeflow.evolution.AlignmentFormat attribute) (treeflow.evolution.seqio.AlignmentFormat attribute) FiniteDiscreteDistribution (class in treeflow.distributions.discrete) fit_fixed_topology_maximum_likelihood_sgd() (in module treeflow.model.ml) fit_fixed_topology_variational_approximation() (in module treeflow.vi.fixed_topology_advi) fit_surrogate_posterior() (in module treeflow.debug.minimize_eager) FixedTopologyRootedTreeBijector (class in treeflow.bijectors.fixed_topology_bijector) flatten_samples_to_dict() (in module treeflow.model.io) flatten_tensor_to_1d_slices() (in module treeflow.model.io) float_constant() (in module treeflow) (in module treeflow.tf_util) (in module treeflow.tf_util.dtype_util) forward() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) forward_dtype() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) forward_event_ndims() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) forward_event_shape() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method)

forward_event_shape_tensor() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) forward_log_det_jacobian() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) forward_min_event_ndims (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) free_params() (treeflow.model.phylo_model.PhyloModel method) (treeflow.model.PhyloModel method) (treeflow.PhyloModel method) frequencies() (treeflow.evolution.substitution.nucleotide.jc.JC static method) from_parameters() (treeflow.bijectors.highway_flow.HighwayFlow class method) fromkeys() (treeflow.tree.taxon_set.DictTaxonSet method)

G

get() (treeflow.tree.taxon_set.DictTaxonSet method) get_anchor_heights() (in module treeflow.traversal.anchor_heights) get_anchor_heights_tensor() (in module treeflow.traversal.anchor_heights) get_base_distribution() (in module treeflow.model.approximation.mean_field) get_batch_transition_probabilities_eigen() (in module treeflow.evolution.substitution.probabilities) get_cascading_flows_tree_approximation() (in module treeflow.model.approximation.cascading_flows) get_clock_model_rates() (in module treeflow.model.phylo_model) get_codon_partitioned_sequence_array() (treeflow.Alignment method) (treeflow.evolution.Alignment method) (treeflow.evolution.seqio.Alignment method) (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) get_codon_partitioned_sequence_tensor() (treeflow.Alignment method) (treeflow.evolution.Alignment method) (treeflow.evolution.seqio.Alignment method) (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) get_common_ancestors() (in module treeflow.evolution.calibration.mrca) get_compressed_alignment() (treeflow.Alignment method) (treeflow.evolution.Alignment method) (treeflow.evolution.seqio.Alignment method) (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) get_constant_coalescent_computation() (in module treeflow.cli.benchmark) get_default_event_space_bijector() (in module treeflow.model.event_shape_bijector) get_discrete_gamma_site_rate_distribution() (in module treeflow.model.phylo_model) get_discrete_weibull_site_rate_distribution() (in module treeflow.model.phylo_model) get_encoded_sequence_array() (treeflow.Alignment method) (treeflow.evolution.Alignment method) (treeflow.evolution.seqio.Alignment method) (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) get_encoded_sequence_tensor() (treeflow.Alignment method) (treeflow.evolution.Alignment method) (treeflow.evolution.seqio.Alignment method) (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) get_event_ndims() (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology class method) get_event_shape_and_space_bijector() (in module treeflow.model.event_shape_bijector) get_fixed_topology_bijector() (in module treeflow.model.event_shape_bijector) get_fixed_topology_event_shape() (in module treeflow.model.event_shape_bijector) get_fixed_topology_event_shape_and_space_bijector() (in module treeflow.model.event_shape_bijector) get_fixed_topology_inverse_autoregressive_flow_approximation() (in module treeflow.model.approximation.iaf) get_fixed_topology_joint_bijector() (in module treeflow.model.event_shape_bijector) get_fixed_topology_mean_field_approximation() (in module treeflow.model.approximation.mean_field) get_gradient_fn() (in module treeflow.cli.benchmark) get_inverse_autoregressive_flow_approximation() (in module treeflow.model.approximation.iaf) get_mean_field_approximation() (in module treeflow.model.approximation.mean_field) get_mean_field_operator_classes() (in module treeflow.model.approximation.mean_field) get_mrca_index() (in module treeflow.evolution.calibration.mrca) (treeflow.evolution.calibration.calibration.MRCACalibration method)

get_mrca_index_array() (treeflow.evolution.calibration.calibration.MRCACalibrationSet method) get_mrca_index_tensor() (treeflow.evolution.calibration.calibration.MRCACalibrationSet method) get_normal_mean() (treeflow.evolution.calibration.calibration.MRCACalibration method) get_normal_mean_array() (treeflow.evolution.calibration.calibration.MRCACalibrationSet method) get_normal_mean_tensor() (treeflow.evolution.calibration.calibration.MRCACalibrationSet method) get_normal_sd() (treeflow.evolution.calibration.calibration.MRCACalibration method) get_normal_sd_array() (treeflow.evolution.calibration.calibration.MRCACalibrationSet method) get_normal_sd_tensor() (treeflow.evolution.calibration.calibration.MRCACalibrationSet method) get_params() (in module treeflow.model.phylo_model) get_prefer_static_rank() (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology method) get_prior() (in module treeflow.model.phylo_model) get_ratio_transform_computation() (in module treeflow.cli.benchmark) get_ratio_transform_jacobian_computation() (in module treeflow.cli.benchmark) get_relaxed_lognormal_clock_rate_distribution() (in module treeflow.model.phylo_model) get_sequence_distribution() (in module treeflow.model.phylo_model) get_site_rate_distribution() (in module treeflow.model.phylo_model) get_strict_clock_rates() (in module treeflow.model.phylo_model) get_subst_model() (in module treeflow.model.phylo_model) get_subst_model_params() (in module treeflow.model.phylo_model) get_trainable_highway_flow_parameters() (in module treeflow.model.approximation.cascading_flows) get_trainable_shift_bijector() (in module treeflow.model.approximation.mean_field) get_transition_probabilities_eigen() (in module treeflow.evolution.substitution.probabilities) get_transition_probabilities_tree() (in module treeflow.evolution.substitution.probabilities) get_tree_likelihood_computation() (in module treeflow.cli.benchmark) get_tree_likelihood_gtr_computation() (in module treeflow.cli.benchmark) get_tree_model() (in module treeflow.model.phylo_model) get_tree_vars() (in module treeflow.cli.inference_common) get_unconstrained_init_values() (in module treeflow.model.event_shape_bijector) get_unrooted_tree() (treeflow.tree.base_tree.AbstractTree method) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree method) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs method) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree method) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree method) (treeflow.tree.unrooted.base_unrooted_tree.AbstractUnrootedTree method) (treeflow.tree.unrooted.numpy_unrooted_tree.NumpyUnrootedTree method) (treeflow.tree.unrooted.tensorflow_unrooted_tree.TensorflowUnrootedTree method) get_weights_array() (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) get_weights_tensor() (treeflow.evolution.seqio.WeightedAlignment method) (treeflow.evolution.WeightedAlignment method) (treeflow.WeightedAlignment method) graph_parents (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) GTR (class in treeflow.evolution.substitution.nucleotide.gtr)

H

H (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) has_batch_dimensions() (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology method) heights (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree property) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree property) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree property) highway_flow_bijector_func() (in module treeflow.bijectors.highway_flow_node_bijector)

highway_flow_root_bijector_func() (in module treeflow.bijectors.highway_flow_node_bijector) HighwayActivationLayer (class in treeflow.bijectors.highway_flow) HighwayFlow (class in treeflow.bijectors.highway_flow) HighwayFlowNodeBijector (class in treeflow.bijectors.highway_flow_node_bijector) HighwayFlowParameters (class in treeflow.bijectors.highway_flow) HighwayFlowParametersFromUnconstrained (class in treeflow.model.approximation.cascading_flows) HKY (class in treeflow.evolution.substitution.nucleotide.hky)

I

index() (treeflow.tree.taxon_set.TupleTaxonSet method) (treeflow.vi.util.VIResults method) InitialValueParseError inverse() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) inverse_dtype() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) inverse_eigenvectors (treeflow.evolution.substitution.eigendecomposition.Eigendecomposition attribute), [1] inverse_event_ndims() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) inverse_event_shape() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) inverse_event_shape_tensor() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method) inverse_log_det_jacobian() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector method) (treeflow.bijectors.highway_flow.HighwayActivationLayer method) (treeflow.bijectors.highway_flow.HighwayFlow method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector method)

inverse_min_event_ndims (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) inverse_with_nones() (in module treeflow.model.event_shape_bijector) is_constant_jacobian (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) is_non_singular (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) is_positive_definite (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) is_scalar_batch() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) is_scalar_event() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) is_scalar_or_vector_of_type() (in module treeflow.model.phylo_model) is_self_adjoint (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) is_square (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) items() (treeflow.tree.taxon_set.DictTaxonSet method)

J

JC (class in treeflow.evolution.substitution.nucleotide.jc)

K

keys() (treeflow.tree.taxon_set.DictTaxonSet method) kl_divergence() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

L

L (treeflow.bijectors.highway_flow.HighwayFlowParameters attribute) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained attribute) lambd (treeflow.bijectors.highway_flow.HighwayFlowParameters attribute) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained attribute) LeafCTMC (class in treeflow.distributions) (class in treeflow.distributions.leaf_ctmc) LinearGaussianPostorderNodeMarkovChain (class in treeflow.distributions.markov_chain.linear_gaussian) LinearOperatorUpperTriangular (class in treeflow.tf_util.linear_operator_upper_triangular) log_abs_determinant() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) log_cdf() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) log_prob() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

log_survival_function() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) loss (treeflow.vi.util.VIResults attribute)

M

make_progress_bar_trace_fn() (in module treeflow.vi.progress_bar) make_trainable() (in module treeflow.model.approximation.mean_field) matmul() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) matvec() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) mean() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) min_num_steps (treeflow.debug.nonfinite_convergence_criterion.NonfiniteConvergenceCriterion property) (treeflow.vi.convergence_criteria.nonfinite.NonfiniteConvergenceCriterion property) minimize_eager() (in module treeflow.debug.minimize_eager) mixture_distribution (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) mode() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) module treeflow treeflow.acceleration treeflow.acceleration.bito treeflow.bijectors treeflow.bijectors.fixed_topology_bijector treeflow.bijectors.highway_flow treeflow.bijectors.highway_flow_node_bijector treeflow.bijectors.node_height_ratio_bijector treeflow.bijectors.preorder_node_bijector treeflow.bijectors.tree_ratio_bijector treeflow.cli treeflow.cli.benchmark treeflow.cli.inference_common treeflow.cli.ml treeflow.cli.vi treeflow.debug treeflow.debug.minimize_eager treeflow.debug.nonfinite_convergence_criterion treeflow.distributions treeflow.distributions.discrete treeflow.distributions.discrete_parameter_mixture treeflow.distributions.discretized treeflow.distributions.leaf_ctmc treeflow.distributions.markov_chain treeflow.distributions.markov_chain.linear_gaussian treeflow.distributions.markov_chain.postorder treeflow.distributions.sample_weighted treeflow.distributions.tree treeflow.distributions.tree.base_tree_distribution treeflow.distributions.tree.birthdeath treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling treeflow.distributions.tree.birthdeath.yule treeflow.distributions.tree.coalescent treeflow.distributions.tree.coalescent.constant_coalescent treeflow.distributions.tree.rooted_tree_distribution treeflow.evolution treeflow.evolution.calibration treeflow.evolution.calibration.calibration treeflow.evolution.calibration.mrca treeflow.evolution.seqio treeflow.evolution.substitution treeflow.evolution.substitution.base_substitution_model treeflow.evolution.substitution.eigendecomposition treeflow.evolution.substitution.nucleotide treeflow.evolution.substitution.nucleotide.alphabet treeflow.evolution.substitution.nucleotide.gtr treeflow.evolution.substitution.nucleotide.hky treeflow.evolution.substitution.nucleotide.jc treeflow.evolution.substitution.probabilities treeflow.evolution.substitution.util treeflow.model treeflow.model.approximation treeflow.model.approximation.cascading_flows treeflow.model.approximation.iaf treeflow.model.approximation.mean_field treeflow.model.event_shape_bijector treeflow.model.io treeflow.model.ml treeflow.model.phylo_model treeflow.model.structured_approximation treeflow.tf_util treeflow.tf_util.attrs treeflow.tf_util.dtype_util treeflow.tf_util.linear_operator_upper_triangular treeflow.tf_util.vectorize treeflow.traversal treeflow.traversal.anchor_heights treeflow.traversal.phylo_likelihood treeflow.traversal.postorder treeflow.traversal.preorder treeflow.traversal.ratio_transform treeflow.tree treeflow.tree.base_tree treeflow.tree.io treeflow.tree.rooted treeflow.tree.rooted.base_rooted_tree treeflow.tree.rooted.numpy_rooted_tree treeflow.tree.rooted.tensorflow_rooted_tree treeflow.tree.taxon_set treeflow.tree.topology treeflow.tree.topology.base_tree_topology treeflow.tree.topology.numpy_topology_operations treeflow.tree.topology.numpy_tree_topology treeflow.tree.topology.tensorflow_tree_topology treeflow.tree.unrooted treeflow.tree.unrooted.base_unrooted_tree treeflow.tree.unrooted.numpy_unrooted_tree treeflow.tree.unrooted.tensorflow_unrooted_tree treeflow.vi treeflow.vi.convergence_criteria treeflow.vi.convergence_criteria.nonfinite treeflow.vi.fixed_topology_advi treeflow.vi.marginal_likelihood treeflow.vi.optimizers treeflow.vi.optimizers.robust_optimizer treeflow.vi.progress_bar treeflow.vi.util

move_indices_to_outside() (in module treeflow.traversal.phylo_likelihood) move_outside_axis_to_inside() (in module treeflow.traversal.ratio_transform) MRCACalibration (class in treeflow.evolution.calibration.calibration) MRCACalibrationSet (class in treeflow.evolution.calibration.calibration)

N

name (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.debug.nonfinite_convergence_criterion.NonfiniteConvergenceCriterion property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) (treeflow.vi.convergence_criteria.nonfinite.NonfiniteConvergenceCriterion property) name_scope (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property)

NEXML (treeflow.AlignmentFormat attribute) (treeflow.evolution.AlignmentFormat attribute) (treeflow.evolution.seqio.AlignmentFormat attribute) NEXUS (treeflow.AlignmentFormat attribute) (treeflow.evolution.AlignmentFormat attribute) (treeflow.evolution.seqio.AlignmentFormat attribute) node_child_indices (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology property) node_count (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology property) node_heights (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree attribute) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs attribute) (treeflow.tree.rooted.base_rooted_tree.BaseRootedTree attribute) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree attribute) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree attribute) node_parent_indices (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector attribute) NodeHeightRatioBijector (class in treeflow.bijectors.node_height_ratio_bijector) NodeHeightRatioChainBijector (class in treeflow.bijectors.node_height_ratio_bijector) non_trainable_variables (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) NonfiniteConvergenceCriterion (class in treeflow.debug.nonfinite_convergence_criterion) (class in treeflow.vi.convergence_criteria.nonfinite) normal_natural_params_to_loc_and_scale() (in module treeflow.model.structured_approximation) normalised_support (treeflow.distributions.discrete.FiniteDiscreteDistribution property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) NUCLEOTIDE (treeflow.AlignmentType attribute) (treeflow.evolution.AlignmentType attribute) (treeflow.evolution.seqio.AlignmentType attribute) numpy() (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree method) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology method) NumpyRootedTree (class in treeflow.tree.rooted.numpy_rooted_tree) NumpyTreeTopology (class in treeflow.tree.topology.numpy_tree_topology) NumpyUnrootedTree (class in treeflow.tree.unrooted.numpy_unrooted_tree)

O

one_step() (treeflow.debug.nonfinite_convergence_criterion.NonfiniteConvergenceCriterion method) (treeflow.vi.convergence_criteria.nonfinite.NonfiniteConvergenceCriterion method)

P

pack_matrix() (in module treeflow.evolution.substitution.util) pack_matrix_transposed() (in module treeflow.evolution.substitution.util) param_shapes() (treeflow.distributions.BirthDeathContemporarySampling class method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture class method) (treeflow.distributions.DiscreteParameterMixture class method) (treeflow.distributions.discretized.DiscretizedDistribution class method) (treeflow.distributions.DiscretizedDistribution class method) (treeflow.distributions.leaf_ctmc.LeafCTMC class method) (treeflow.distributions.LeafCTMC class method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain class method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain class method) (treeflow.distributions.sample_weighted.SampleWeighted class method) (treeflow.distributions.SampleWeighted class method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution class method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.birthdeath.yule.Yule class method) (treeflow.distributions.tree.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent class method) (treeflow.distributions.tree.ConstantCoalescent class method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution class method) (treeflow.distributions.tree.Yule class method) param_static_shapes() (treeflow.distributions.BirthDeathContemporarySampling class method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture class method) (treeflow.distributions.DiscreteParameterMixture class method) (treeflow.distributions.discretized.DiscretizedDistribution class method) (treeflow.distributions.DiscretizedDistribution class method) (treeflow.distributions.leaf_ctmc.LeafCTMC class method) (treeflow.distributions.LeafCTMC class method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain class method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain class method) (treeflow.distributions.sample_weighted.SampleWeighted class method) (treeflow.distributions.SampleWeighted class method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution class method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.birthdeath.yule.Yule class method) (treeflow.distributions.tree.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent class method) (treeflow.distributions.tree.ConstantCoalescent class method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution class method) (treeflow.distributions.tree.Yule class method) parameter_properties() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector class method) (treeflow.bijectors.highway_flow.HighwayActivationLayer class method) (treeflow.bijectors.highway_flow.HighwayFlow class method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer class method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector class method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector class method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector class method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector class method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector class method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector class method) (treeflow.distributions.BirthDeathContemporarySampling class method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture class method) (treeflow.distributions.DiscreteParameterMixture class method) (treeflow.distributions.discretized.DiscretizedDistribution class method) (treeflow.distributions.DiscretizedDistribution class method) (treeflow.distributions.leaf_ctmc.LeafCTMC class method) (treeflow.distributions.LeafCTMC class method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain class method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain class method) (treeflow.distributions.sample_weighted.SampleWeighted class method) (treeflow.distributions.SampleWeighted class method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution class method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.birthdeath.yule.Yule class method) (treeflow.distributions.tree.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent class method) (treeflow.distributions.tree.ConstantCoalescent class method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution class method) (treeflow.distributions.tree.Yule class method) parameters (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) (treeflow.vi.util.VIResults attribute)

parent_indices (treeflow.tree.topology.base_tree_topology.AbstractTreeTopology attribute) (treeflow.tree.topology.base_tree_topology.BaseTreeTopology attribute) (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology attribute) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology attribute) parse_init_value() (in module treeflow.cli.inference_common) parse_init_values() (in module treeflow.cli.inference_common) parse_model() (in module treeflow.model.phylo_model) parse_newick() (in module treeflow) (in module treeflow.tree) (in module treeflow.tree.io) pattern_count (treeflow.Alignment property) (treeflow.evolution.Alignment property) (treeflow.evolution.seqio.Alignment property) (treeflow.evolution.seqio.WeightedAlignment property) (treeflow.evolution.WeightedAlignment property) (treeflow.WeightedAlignment property) PHYLIP (treeflow.AlignmentFormat attribute) (treeflow.evolution.AlignmentFormat attribute) (treeflow.evolution.seqio.AlignmentFormat attribute) phylo_model_to_joint_distribution() (in module treeflow) (in module treeflow.model) (in module treeflow.model.phylo_model) phylogenetic_likelihood() (in module treeflow.traversal.phylo_likelihood) PhyloModel (class in treeflow) (class in treeflow.model) (class in treeflow.model.phylo_model) PhyloModelParseError pop() (treeflow.tree.taxon_set.DictTaxonSet method) popitem() (treeflow.tree.taxon_set.DictTaxonSet method) posterior_marginal() (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) posterior_mode() (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) postorder_node_indices (treeflow.tree.topology.base_tree_topology.AbstractTreeTopology property) (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology property) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology property) postorder_node_traversal() (in module treeflow.traversal.postorder) PostorderNodeMarkovChain (class in treeflow.distributions.markov_chain.postorder) PostorderTopologyData (class in treeflow.traversal.postorder) preorder_indices (treeflow.tree.topology.base_tree_topology.AbstractTreeTopology property) (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology property) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology attribute) preorder_node_indices (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology property) preorder_traversal() (in module treeflow.traversal.preorder) PreorderNodeBijector (class in treeflow.bijectors.preorder_node_bijector) prob() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) probabilities (treeflow.distributions.discrete.FiniteDiscreteDistribution property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) ProgressBarFunc (class in treeflow.vi.progress_bar) ProgressBarTraceFunctionContextManager (class in treeflow.vi.progress_bar) PROTEIN (treeflow.AlignmentType attribute) (treeflow.evolution.AlignmentType attribute) (treeflow.evolution.seqio.AlignmentType attribute) push_through_flow() (in module treeflow.bijectors.highway_flow_node_bijector)

Q

q() (treeflow.evolution.substitution.base_substitution_model.EigendecompositionSubstitutionModel method) (treeflow.evolution.substitution.base_substitution_model.SubstitutionModel method) (treeflow.evolution.substitution.nucleotide.gtr.GTR method) (treeflow.evolution.substitution.nucleotide.hky.HKY method) (treeflow.evolution.substitution.nucleotide.jc.JC method) q_norm() (treeflow.evolution.substitution.base_substitution_model.EigendecompositionSubstitutionModel method) (treeflow.evolution.substitution.base_substitution_model.SubstitutionModel method) (treeflow.evolution.substitution.nucleotide.gtr.GTR method) (treeflow.evolution.substitution.nucleotide.hky.HKY method) (treeflow.evolution.substitution.nucleotide.jc.JC method) quantile() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

R

range_dimension (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) range_dimension_tensor() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) rank_to_has_batch_dimensions() (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology class method) ratios_to_node_heights() (in module treeflow.traversal.ratio_transform) relaxed_clock() (treeflow.model.phylo_model.PhyloModel method) (treeflow.model.PhyloModel method) (treeflow.PhyloModel method) remove_zero_edges() (in module treeflow.tree.io) reparameterization_type (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property)

reshape_structure() (in module treeflow.tf_util.vectorize) RobustOptimizer (class in treeflow.vi.optimizers.robust_optimizer) root_height (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree property) RootedTreeBijector (class in treeflow.bijectors.tree_ratio_bijector) RootedTreeDistribution (class in treeflow.distributions.tree.rooted_tree_distribution)

S

sample() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) sample_shape (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) SampleWeighted (class in treeflow.distributions) (class in treeflow.distributions.sample_weighted) sampling_times (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.Yule property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree attribute) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs attribute) (treeflow.tree.rooted.base_rooted_tree.BaseRootedTree attribute) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree attribute) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree attribute) setdefault() (treeflow.tree.taxon_set.DictTaxonSet method) shape (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) shape_tensor() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) solve() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) solvevec() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) stddev() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

submodules (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) SubstitutionModel (class in treeflow.evolution.substitution.base_substitution_model) support (treeflow.distributions.discrete.FiniteDiscreteDistribution property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) support_size (treeflow.distributions.discrete.FiniteDiscreteDistribution property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) survival_function() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

T

taxon_count (treeflow.Alignment property) (treeflow.evolution.Alignment property) (treeflow.evolution.seqio.Alignment property) (treeflow.evolution.seqio.WeightedAlignment property) (treeflow.evolution.WeightedAlignment property) (treeflow.tree.base_tree.AbstractTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs property) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree property) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree property) (treeflow.tree.topology.base_tree_topology.AbstractTreeTopology property) (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology property) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology property) (treeflow.tree.unrooted.base_unrooted_tree.AbstractUnrootedTree property) (treeflow.tree.unrooted.numpy_unrooted_tree.NumpyUnrootedTree property) (treeflow.tree.unrooted.tensorflow_unrooted_tree.TensorflowUnrootedTree property) (treeflow.WeightedAlignment property) taxon_set (treeflow.tree.base_tree.AbstractTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs property) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree property) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree property) (treeflow.tree.topology.base_tree_topology.AbstractTreeTopology property) (treeflow.tree.topology.numpy_tree_topology.NumpyTreeTopology property) (treeflow.tree.topology.tensorflow_tree_topology.TensorflowTreeTopology property) (treeflow.tree.unrooted.base_unrooted_tree.AbstractUnrootedTree property) (treeflow.tree.unrooted.numpy_unrooted_tree.NumpyUnrootedTree property) (treeflow.tree.unrooted.tensorflow_unrooted_tree.TensorflowUnrootedTree property) TaxonSet (class in treeflow.tree.taxon_set) tensor_rank (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) tensor_rank_tensor() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) tensor_taxon_count() (in module treeflow.tree.topology.tensorflow_tree_topology) TensorflowRootedTree (class in treeflow.tree.rooted.tensorflow_rooted_tree) TensorflowTreeTopology (class in treeflow.tree.topology.tensorflow_tree_topology) TensorflowUnrootedTree (class in treeflow.tree.unrooted.tensorflow_unrooted_tree) time_fn() (in module treeflow.cli.benchmark) to_dense() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) topology (treeflow.tree.base_tree.AbstractTree property) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree attribute) (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTreeAttrs attribute) (treeflow.tree.rooted.base_rooted_tree.BaseRootedTree attribute) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree attribute) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree attribute) (treeflow.tree.unrooted.base_unrooted_tree.AbstractUnrootedTree attribute) (treeflow.tree.unrooted.base_unrooted_tree.BaseUnrootedTree attribute) (treeflow.tree.unrooted.numpy_unrooted_tree.NumpyUnrootedTree attribute) (treeflow.tree.unrooted.tensorflow_unrooted_tree.TensorflowUnrootedTree attribute) trace() (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular method) trainable_variables (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) tree_from_arrays() (in module treeflow.tree.rooted.tensorflow_rooted_tree) treeflow module treeflow.acceleration module treeflow.acceleration.bito module treeflow.bijectors module treeflow.bijectors.fixed_topology_bijector module treeflow.bijectors.highway_flow module treeflow.bijectors.highway_flow_node_bijector module treeflow.bijectors.node_height_ratio_bijector module treeflow.bijectors.preorder_node_bijector module treeflow.bijectors.tree_ratio_bijector module treeflow.cli module treeflow.cli.benchmark module treeflow.cli.inference_common module treeflow.cli.ml module treeflow.cli.vi module treeflow.debug module treeflow.debug.minimize_eager module treeflow.debug.nonfinite_convergence_criterion module treeflow.distributions module treeflow.distributions.discrete module treeflow.distributions.discrete_parameter_mixture module treeflow.distributions.discretized module treeflow.distributions.leaf_ctmc module treeflow.distributions.markov_chain module treeflow.distributions.markov_chain.linear_gaussian module treeflow.distributions.markov_chain.postorder module treeflow.distributions.sample_weighted module treeflow.distributions.tree module treeflow.distributions.tree.base_tree_distribution module treeflow.distributions.tree.birthdeath module treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling module treeflow.distributions.tree.birthdeath.yule module treeflow.distributions.tree.coalescent module treeflow.distributions.tree.coalescent.constant_coalescent module treeflow.distributions.tree.rooted_tree_distribution module treeflow.evolution module treeflow.evolution.calibration module treeflow.evolution.calibration.calibration module treeflow.evolution.calibration.mrca module treeflow.evolution.seqio module treeflow.evolution.substitution module treeflow.evolution.substitution.base_substitution_model module

treeflow.evolution.substitution.eigendecomposition module treeflow.evolution.substitution.nucleotide module treeflow.evolution.substitution.nucleotide.alphabet module treeflow.evolution.substitution.nucleotide.gtr module treeflow.evolution.substitution.nucleotide.hky module treeflow.evolution.substitution.nucleotide.jc module treeflow.evolution.substitution.probabilities module treeflow.evolution.substitution.util module treeflow.model module treeflow.model.approximation module treeflow.model.approximation.cascading_flows module treeflow.model.approximation.iaf module treeflow.model.approximation.mean_field module treeflow.model.event_shape_bijector module treeflow.model.io module treeflow.model.ml module treeflow.model.phylo_model module treeflow.model.structured_approximation module treeflow.tf_util module treeflow.tf_util.attrs module treeflow.tf_util.dtype_util module treeflow.tf_util.linear_operator_upper_triangular module treeflow.tf_util.vectorize module treeflow.traversal module treeflow.traversal.anchor_heights module treeflow.traversal.phylo_likelihood module treeflow.traversal.postorder module treeflow.traversal.preorder module treeflow.traversal.ratio_transform module treeflow.tree module treeflow.tree.base_tree module treeflow.tree.io module treeflow.tree.rooted module treeflow.tree.rooted.base_rooted_tree module treeflow.tree.rooted.numpy_rooted_tree module treeflow.tree.rooted.tensorflow_rooted_tree module treeflow.tree.taxon_set module treeflow.tree.topology module treeflow.tree.topology.base_tree_topology module treeflow.tree.topology.numpy_topology_operations module treeflow.tree.topology.numpy_tree_topology module treeflow.tree.topology.tensorflow_tree_topology module treeflow.tree.unrooted module treeflow.tree.unrooted.base_unrooted_tree module treeflow.tree.unrooted.numpy_unrooted_tree module treeflow.tree.unrooted.tensorflow_unrooted_tree module treeflow.vi module treeflow.vi.convergence_criteria module treeflow.vi.convergence_criteria.nonfinite module treeflow.vi.fixed_topology_advi module treeflow.vi.marginal_likelihood module treeflow.vi.optimizers module treeflow.vi.optimizers.robust_optimizer module treeflow.vi.progress_bar module treeflow.vi.util module treeflow_ml command line option --alignment-format --init-values --input --learning-rate --model-file --no-progress-bar --num-steps --optimizer --progress-bar --subnewick-format --topology --trace-output --tree-output --variables-output -i -m -n -o -r -t treeflow_vi command line option --alignment-format --convergence-criterion --elbo-samples --init-values --input --learning-rate --model-file --n-output-samples --no-progress-bar --num-steps --optimizer --progress-bar --samples-output --seed --subnewick-format --topology --trace-output --tree-samples-output --variational-approximation -c -i -m -n -o -r -s -t -va TreeRatioBijector (class in treeflow.bijectors.tree_ratio_bijector) TriangularHighwayLayer (class in treeflow.bijectors.highway_flow) triu (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property) TupleTaxonSet (class in treeflow.tree.taxon_set)

U

U (treeflow.bijectors.highway_flow.HighwayFlowParameters attribute) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained attribute) unnormalized_log_prob() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method)

UnrootedTreeType (treeflow.tree.rooted.base_rooted_tree.AbstractRootedTree attribute) (treeflow.tree.rooted.numpy_rooted_tree.NumpyRootedTree attribute) (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree attribute) update() (treeflow.tree.taxon_set.DictTaxonSet method) update_trace_fn() (in module treeflow.vi.progress_bar)

V

validate_args (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) validate_event_size (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) values() (treeflow.tree.taxon_set.DictTaxonSet method) variables (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector property) (treeflow.bijectors.highway_flow.HighwayActivationLayer property) (treeflow.bijectors.highway_flow.HighwayFlow property) (treeflow.bijectors.highway_flow.TriangularHighwayLayer property) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector property) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector property) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector property) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector property) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector property) (treeflow.distributions.BirthDeathContemporarySampling property) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture property) (treeflow.distributions.DiscreteParameterMixture property) (treeflow.distributions.discretized.DiscretizedDistribution property) (treeflow.distributions.DiscretizedDistribution property) (treeflow.distributions.leaf_ctmc.LeafCTMC property) (treeflow.distributions.LeafCTMC property) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain property) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain property) (treeflow.distributions.sample_weighted.SampleWeighted property) (treeflow.distributions.SampleWeighted property) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution property) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling property) (treeflow.distributions.tree.birthdeath.yule.Yule property) (treeflow.distributions.tree.BirthDeathContemporarySampling property) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent property) (treeflow.distributions.tree.ConstantCoalescent property) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution property) (treeflow.distributions.tree.Yule property) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained property) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular property)

variance() (treeflow.distributions.BirthDeathContemporarySampling method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture method) (treeflow.distributions.DiscreteParameterMixture method) (treeflow.distributions.discretized.DiscretizedDistribution method) (treeflow.distributions.DiscretizedDistribution method) (treeflow.distributions.leaf_ctmc.LeafCTMC method) (treeflow.distributions.LeafCTMC method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain method) (treeflow.distributions.sample_weighted.SampleWeighted method) (treeflow.distributions.SampleWeighted method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling method) (treeflow.distributions.tree.birthdeath.yule.Yule method) (treeflow.distributions.tree.BirthDeathContemporarySampling method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent method) (treeflow.distributions.tree.ConstantCoalescent method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution method) (treeflow.distributions.tree.Yule method) vectorize_over_batch_dims() (in module treeflow.tf_util.vectorize) VIResults (class in treeflow.vi.util)

W

WeightedAlignment (class in treeflow) (class in treeflow.evolution) (class in treeflow.evolution.seqio) with_branch_lengths() (treeflow.tree.unrooted.tensorflow_unrooted_tree.TensorflowUnrootedTree method) with_name_scope() (treeflow.bijectors.fixed_topology_bijector.FixedTopologyRootedTreeBijector class method) (treeflow.bijectors.highway_flow.HighwayActivationLayer class method) (treeflow.bijectors.highway_flow.HighwayFlow class method) (treeflow.bijectors.highway_flow.TriangularHighwayLayer class method) (treeflow.bijectors.highway_flow_node_bijector.HighwayFlowNodeBijector class method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioBijector class method) (treeflow.bijectors.node_height_ratio_bijector.NodeHeightRatioChainBijector class method) (treeflow.bijectors.preorder_node_bijector.PreorderNodeBijector class method) (treeflow.bijectors.tree_ratio_bijector.RootedTreeBijector class method) (treeflow.bijectors.tree_ratio_bijector.TreeRatioBijector class method) (treeflow.distributions.BirthDeathContemporarySampling class method) (treeflow.distributions.discrete_parameter_mixture.DiscreteParameterMixture class method) (treeflow.distributions.DiscreteParameterMixture class method) (treeflow.distributions.discretized.DiscretizedDistribution class method) (treeflow.distributions.DiscretizedDistribution class method) (treeflow.distributions.leaf_ctmc.LeafCTMC class method) (treeflow.distributions.LeafCTMC class method) (treeflow.distributions.markov_chain.linear_gaussian.LinearGaussianPostorderNodeMarkovChain class method) (treeflow.distributions.markov_chain.postorder.PostorderNodeMarkovChain class method) (treeflow.distributions.sample_weighted.SampleWeighted class method) (treeflow.distributions.SampleWeighted class method) (treeflow.distributions.tree.base_tree_distribution.BaseTreeDistribution class method) (treeflow.distributions.tree.birthdeath.birth_death_contemporary_sampling.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.birthdeath.yule.Yule class method) (treeflow.distributions.tree.BirthDeathContemporarySampling class method) (treeflow.distributions.tree.coalescent.constant_coalescent.ConstantCoalescent class method) (treeflow.distributions.tree.ConstantCoalescent class method) (treeflow.distributions.tree.rooted_tree_distribution.RootedTreeDistribution class method) (treeflow.distributions.tree.Yule class method) (treeflow.model.approximation.cascading_flows.HighwayFlowParametersFromUnconstrained class method) (treeflow.tf_util.linear_operator_upper_triangular.LinearOperatorUpperTriangular class method)

with_node_heights() (treeflow.tree.rooted.tensorflow_rooted_tree.TensorflowRootedTree method) with_traceback() (treeflow.cli.inference_common.InitialValueParseError method) (treeflow.model.phylo_model.PhyloModelParseError method) wrap_in_root_if_needed() (in module treeflow.model.phylo_model) write_samples_to_file() (in module treeflow.model.io) write_tensor_trees() (in module treeflow) (in module treeflow.tree) (in module treeflow.tree.io) write_trees() (in module treeflow.cli.inference_common)

Y

Yule (class in treeflow.distributions.tree) (class in treeflow.distributions.tree.birthdeath.yule)