Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W _ __and__() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) __call__() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.EdgeView method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.EdgeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) __contains__() (phylozoo.core.distance.base.DistanceMatrix method) (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.EdgeView method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.EdgeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.sequence.base.MSA method) (phylozoo.core.split.splitsystem.SplitSystem method) (phylozoo.core.triplet.tprofile.TripletProfile method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) __del__() (phylozoo.utils.parallel.MultiprocessingExecutor method) (phylozoo.utils.parallel.ThreadingExecutor method) __eq__() (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.triplet.base.Triplet method) __getitem__() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) __hash__() (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.triplet.base.Triplet method) __iter__() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.EdgeView method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.EdgeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.split.splitsystem.SplitSystem method) (phylozoo.core.triplet.tprofile.TripletProfile method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) __len__() (phylozoo.core.distance.base.DistanceMatrix method) (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.EdgeView method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.EdgeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.sequence.base.MSA method) (phylozoo.core.split.splitsystem.SplitSystem method) (phylozoo.core.triplet.tprofile.TripletProfile method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) __or__() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) __repr__() (phylozoo.core.distance.base.DistanceMatrix method) (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator method) (phylozoo.core.network.sdnetwork.sd_phynetwork.SemiDirectedPhyNetwork method) (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.EdgeView method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.EdgeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.sequence.base.MSA method) (phylozoo.core.split.base.Split method) (phylozoo.core.split.splitsystem.SplitSystem method) (phylozoo.core.split.weighted_splitsystem.WeightedSplitSystem method) (phylozoo.core.triplet.base.Triplet method) (phylozoo.core.triplet.tprofile.TripletProfile method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) (phylozoo.utils.parallel.ParallelConfig method) __setattr__() (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) (phylozoo.core.primitives.partition.Partition method) (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.split.splitsystem.SplitSystem method) (phylozoo.core.triplet.base.Triplet method) (phylozoo.core.triplet.tprofile.TripletProfile method) __str__() (phylozoo.core.distance.base.DistanceMatrix method) (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.sequence.base.MSA method) (phylozoo.core.split.splitsystem.SplitSystem method) (phylozoo.core.split.weighted_splitsystem.WeightedSplitSystem method) (phylozoo.core.triplet.base.Triplet method) (phylozoo.core.triplet.tprofile.TripletProfile method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) _combined (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph attribute) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph attribute) _directed (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph attribute) _graph (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator attribute) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator attribute) (phylozoo.core.network.sdnetwork.sd_phynetwork.SemiDirectedPhyNetwork attribute) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph attribute) _label_to_node (phylozoo.core.network.sdnetwork.sd_phynetwork.SemiDirectedPhyNetwork attribute) _node_to_label (phylozoo.core.network.sdnetwork.sd_phynetwork.SemiDirectedPhyNetwork attribute) _sides (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator attribute) _undirected (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph attribute) A add_directed_edge() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) add_directed_edges_from() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) add_edge() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) add_edges_from() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) add_node() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) add_nodes_from() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) add_undirected_edge() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) add_undirected_edges_from() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) all_level_k_generators() (in module phylozoo.core.network.dnetwork.generator.construction) (in module phylozoo.core.network.sdnetwork.generator.construction) all_profile_taxon_sets() (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) are_neighbors() (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) are_singletons() (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) arrow_head_size (phylozoo.viz.d_multigraph.style.BaseStyle attribute) attach_leaves_to_generator() (in module phylozoo.core.network.dnetwork.generator.attachment) (in module phylozoo.core.network.sdnetwork.generator.attachment) B BaseStyle (class in phylozoo.viz.d_multigraph.style) bi_edge_connected_components() (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) biconnected_components() (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) BidirectedEdgeSide (class in phylozoo.core.network.sdnetwork.generator.side) binary_resolution() (in module phylozoo.core.network.dnetwork.transformations) blobs() (in module phylozoo.core.network.dnetwork.features) (in module phylozoo.core.network.sdnetwork.features) bootstrap() (in module phylozoo.core.sequence.bootstrap) bootstrap_per_gene() (in module phylozoo.core.sequence.bootstrap) C cherry (phylozoo.core.triplet.base.Triplet property) children() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) circular_orderings (phylozoo.core.quartet.base.Quartet property) (phylozoo.core.quartet.qprofile.QuartetProfile property) CircularOrdering (class in phylozoo.core.primitives.circular_ordering) CircularSetOrdering (class in phylozoo.core.primitives.circular_ordering) clear() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) coded_array (phylozoo.core.sequence.base.MSA property) combined_graph (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph property) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph property) connected_components() (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) convert() (phylozoo.utils.io.mixin.IOMixin class method) convert_string() (phylozoo.utils.io.mixin.IOMixin class method) copy() (phylozoo.core.distance.base.DistanceMatrix method) (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.network.sdnetwork.sd_phynetwork.SemiDirectedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.sequence.base.MSA method) (phylozoo.core.triplet.base.Triplet method) (phylozoo.viz.dnetwork.style.DNetStyle method) (phylozoo.viz.sdnetwork.style.SDNetStyle method) cut_edges() (in module phylozoo.core.network.dnetwork.features) (in module phylozoo.core.network.sdnetwork.features) (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) cut_vertices() (in module phylozoo.core.network.dnetwork.features) (in module phylozoo.core.network.sdnetwork.features) (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) D default_style() (in module phylozoo.viz.d_multigraph.style) (in module phylozoo.viz.dnetwork.style) (in module phylozoo.viz.m_multigraph.style) (in module phylozoo.viz.sdnetwork.style) degree() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) detect_format() (phylozoo.utils.io.registry.FormatRegistry class method) dgenerator_to_sdgenerator() (in module phylozoo.core.network.sdnetwork.generator.construction) digraph_to_directedmultigraph() (in module phylozoo.core.primitives.d_multigraph.conversions) directed_edge_sides (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) directed_edges (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph property) directed_edges_iter() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) DirectedGenerator (class in phylozoo.core.network.dnetwork.generator.base) DirectedMultiGraph (class in phylozoo.core.primitives.d_multigraph.base) DirectedMultiGraph.EdgeView (class in phylozoo.core.primitives.d_multigraph.base) DirectedMultiGraph.NodeView (class in phylozoo.core.primitives.d_multigraph.base) directedmultigraph_to_mixedmultigraph() (in module phylozoo.core.primitives.m_multigraph.conversions) DirectedPhyNetwork (class in phylozoo.core.network.dnetwork.base) DirEdgeSide (class in phylozoo.core.network.dnetwork.generator.side) displayed_quartets() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) displayed_splits() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) displayed_trees() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) displayed_triplets() (in module phylozoo.core.network.dnetwork.derivations) DistanceMatrix (class in phylozoo.core.distance.base) distances() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) distances_from_splitsystem() (in module phylozoo.core.split.algorithms) DMGraphStyle (class in phylozoo.viz.d_multigraph.style) DNetStyle (class in phylozoo.viz.dnetwork.style) dnetwork_from_graph() (in module phylozoo.core.network.dnetwork.conversions) E edge_color (phylozoo.viz.d_multigraph.style.BaseStyle attribute) edge_sides (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) edge_width (phylozoo.viz.d_multigraph.style.BaseStyle attribute) edges (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph property) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph property) edges_iter() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) EdgeSide (class in phylozoo.core.network.dnetwork.generator.side) elements (phylozoo.core.primitives.partition.Partition property) (phylozoo.core.split.base.Split attribute) (phylozoo.core.split.splitsystem.SplitSystem property) ensure_directory_exists() (in module phylozoo.utils.io.file_ops) F FormatRegistry (class in phylozoo.utils.io.registry) from_coded_array() (phylozoo.core.sequence.base.MSA class method) from_csv() (in module phylozoo.core.distance.io) from_dot() (in module phylozoo.core.network.dnetwork.io) (in module phylozoo.core.primitives.d_multigraph.io) from_edgelist() (in module phylozoo.core.primitives.d_multigraph.io) from_enewick() (in module phylozoo.core.network.dnetwork.io) (in module phylozoo.core.network.sdnetwork.io) from_fasta() (in module phylozoo.core.sequence.io) from_nexus() (in module phylozoo.core.distance.io) (in module phylozoo.core.sequence.io) from_nexus_split_system() (in module phylozoo.core.split.io) from_nexus_weighted_split_system() (in module phylozoo.core.split.io) from_phylip() (in module phylozoo.core.distance.io) from_phylozoo_dot() (in module phylozoo.core.network.sdnetwork.io) (in module phylozoo.core.primitives.m_multigraph.io) from_string() (phylozoo.utils.io.mixin.IOMixin class method) G generate_node_ids() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) generators_from_network() (in module phylozoo.core.network.dnetwork.generator.base) get_bootstrap() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_branch_length() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_distance() (phylozoo.core.distance.base.DistanceMatrix method) get_edge_attribute() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_executor() (phylozoo.utils.parallel.ParallelConfig method) get_gamma() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_index() (phylozoo.core.distance.base.DistanceMatrix method) get_label() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_network_attribute() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_node_attribute() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_node_id() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) get_part() (phylozoo.core.primitives.partition.Partition method) get_profile() (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) get_profile_weight() (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) get_reader() (phylozoo.utils.io.registry.FormatRegistry class method) get_sequence() (phylozoo.core.sequence.base.MSA method) get_sequences() (phylozoo.core.sequence.base.MSA method) get_weight() (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.split.weighted_splitsystem.WeightedSplitSystem method) (phylozoo.core.triplet.tprofile.TripletProfile method) get_writer() (phylozoo.utils.io.registry.FormatRegistry class method) graph (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) graph_to_mixedmultigraph() (in module phylozoo.core.primitives.m_multigraph.conversions) H hamming_distances() (in module phylozoo.core.sequence.distances) has_all_trivial_splits() (in module phylozoo.core.split.classifications) has_edge() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) has_parallel_edges() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) has_profile() (phylozoo.core.quartet.qprofileset.QuartetProfileSet method) (phylozoo.core.triplet.tprofileset.TripletProfileSet method) has_self_loops() (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) has_zero_diagonal() (in module phylozoo.core.distance.classifications) hybrid_color (phylozoo.viz.dnetwork.style.DNetStyle attribute) (phylozoo.viz.sdnetwork.style.SDNetStyle attribute) hybrid_edge_color (phylozoo.viz.dnetwork.style.DNetStyle attribute) (phylozoo.viz.sdnetwork.style.SDNetStyle attribute) hybrid_edges (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) hybrid_nodes (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) hybrid_sides (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) HybridSide (class in phylozoo.core.network.dnetwork.generator.side) I identify_parallel_edge() (in module phylozoo.core.primitives.d_multigraph.transformations) (in module phylozoo.core.primitives.m_multigraph.transformations) identify_parallel_edges() (in module phylozoo.core.network.dnetwork.transformations) (in module phylozoo.core.network.sdnetwork.transformations) identify_vertices() (in module phylozoo.core.primitives.d_multigraph.transformations) (in module phylozoo.core.primitives.m_multigraph.transformations) incident_child_edges() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) incident_parent_edges() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) incident_undirected_edges() (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) indegree() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) indices (phylozoo.core.distance.base.DistanceMatrix property) induced_quartetsplits() (in module phylozoo.core.split.algorithms) (phylozoo.core.split.splitsystem.SplitSystem method) induced_splits() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) internal_nodes (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) IOMixin (class in phylozoo.utils.io.mixin) is_all_resolved (phylozoo.core.quartet.qprofileset.QuartetProfileSet property) (phylozoo.core.triplet.tprofileset.TripletProfileSet property) is_binary() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) is_compatible() (in module phylozoo.core.split.classifications) is_connected() (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) is_dense (phylozoo.core.quartet.qprofileset.QuartetProfileSet property) (phylozoo.core.triplet.tprofileset.TripletProfileSet property) is_galled() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) is_isomorphic() (in module phylozoo.core.network.dnetwork.isomorphism) (in module phylozoo.core.network.sdnetwork.isomorphism) (in module phylozoo.core.primitives.d_multigraph.isomorphism) (in module phylozoo.core.primitives.m_multigraph.isomorphism) is_kalmanson() (in module phylozoo.core.distance.classifications) is_lsa_network() (in module phylozoo.core.network.dnetwork.classifications) is_metric() (in module phylozoo.core.distance.classifications) is_nonnegative() (in module phylozoo.core.distance.classifications) is_normal() (in module phylozoo.core.network.dnetwork.classifications) is_pairwise_compatible() (in module phylozoo.core.split.classifications) is_pseudo_metric() (in module phylozoo.core.distance.classifications) is_refinement() (phylozoo.core.primitives.partition.Partition method) is_resolved() (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.triplet.base.Triplet method) (phylozoo.core.triplet.tprofile.TripletProfile method) is_simple() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) is_stackfree() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) is_star() (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.triplet.base.Triplet method) is_strongly_treebased() (in module phylozoo.core.network.sdnetwork.classifications) is_strongly_treechild() (in module phylozoo.core.network.sdnetwork.classifications) is_subsplit() (in module phylozoo.core.split.classifications) is_totally_decomposable() (in module phylozoo.core.distance.classifications) is_tree() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) is_tree_compatible() (in module phylozoo.core.split.classifications) is_tree_metric() (in module phylozoo.core.distance.classifications) is_treebased() (in module phylozoo.core.network.dnetwork.classifications) is_treechild() (in module phylozoo.core.network.dnetwork.classifications) is_trivial (phylozoo.core.split.base.Split property) is_trivial() (phylozoo.core.quartet.qprofile.QuartetProfile method) (phylozoo.core.triplet.tprofile.TripletProfile method) is_ultrametric() (in module phylozoo.core.network.dnetwork.classifications) is_weakly_treebased() (in module phylozoo.core.network.sdnetwork.classifications) is_weakly_treechild() (in module phylozoo.core.network.sdnetwork.classifications) IsolatedNodeSide (class in phylozoo.core.network.dnetwork.generator.side) isolation_index() (in module phylozoo.core.distance.decomposition) issubset() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph.NodeView method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph.NodeView method) K k_blobs() (in module phylozoo.core.network.dnetwork.features) (in module phylozoo.core.network.sdnetwork.features) k_taxon_subnetworks() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) key (phylozoo.core.network.dnetwork.generator.side.DirEdgeSide attribute) (phylozoo.core.network.sdnetwork.generator.side.BidirectedEdgeSide attribute) (phylozoo.core.network.sdnetwork.generator.side.UndirEdgeSide attribute) L label_color (phylozoo.viz.d_multigraph.style.BaseStyle attribute) label_font_size (phylozoo.viz.d_multigraph.style.BaseStyle attribute) label_offset (phylozoo.viz.d_multigraph.style.BaseStyle attribute) labels (phylozoo.core.distance.base.DistanceMatrix property) leaf_color (phylozoo.viz.dnetwork.style.DNetStyle attribute) (phylozoo.viz.sdnetwork.style.SDNetStyle attribute) leaf_size (phylozoo.viz.dnetwork.style.DNetStyle attribute) (phylozoo.viz.sdnetwork.style.SDNetStyle attribute) leaves (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) level (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) level() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) load() (phylozoo.utils.io.mixin.IOMixin class method) LSA_node (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) lsa_node() (in module phylozoo.core.network.dnetwork.features) M map() (phylozoo.utils.parallel.MultiprocessingExecutor method) (phylozoo.utils.parallel.ParallelExecutor method) (phylozoo.utils.parallel.SequentialExecutor method) (phylozoo.utils.parallel.ThreadingExecutor method) max_profile_len (phylozoo.core.quartet.qprofileset.QuartetProfileSet property) (phylozoo.core.triplet.tprofileset.TripletProfileSet property) MGraphStyle (class in phylozoo.viz.m_multigraph.style) MixedMultiGraph (class in phylozoo.core.primitives.m_multigraph.base) MixedMultiGraph.EdgeView (class in phylozoo.core.primitives.m_multigraph.base) MixedMultiGraph.NodeView (class in phylozoo.core.primitives.m_multigraph.base) MixedPhyNetwork (class in phylozoo.core.network.sdnetwork.base) module phylozoo.core phylozoo.core.distance phylozoo.core.distance.base phylozoo.core.distance.classifications phylozoo.core.distance.decomposition phylozoo.core.distance.io phylozoo.core.network phylozoo.core.network.dnetwork phylozoo.core.network.dnetwork.base phylozoo.core.network.dnetwork.classifications phylozoo.core.network.dnetwork.conversions phylozoo.core.network.dnetwork.derivations phylozoo.core.network.dnetwork.features phylozoo.core.network.dnetwork.generator phylozoo.core.network.dnetwork.generator.attachment phylozoo.core.network.dnetwork.generator.base phylozoo.core.network.dnetwork.generator.construction phylozoo.core.network.dnetwork.generator.side phylozoo.core.network.dnetwork.io phylozoo.core.network.dnetwork.isomorphism phylozoo.core.network.dnetwork.transformations phylozoo.core.network.sdnetwork phylozoo.core.network.sdnetwork.base phylozoo.core.network.sdnetwork.classifications phylozoo.core.network.sdnetwork.conversions phylozoo.core.network.sdnetwork.derivations phylozoo.core.network.sdnetwork.features phylozoo.core.network.sdnetwork.generator phylozoo.core.network.sdnetwork.generator.attachment phylozoo.core.network.sdnetwork.generator.base phylozoo.core.network.sdnetwork.generator.construction phylozoo.core.network.sdnetwork.generator.side phylozoo.core.network.sdnetwork.io phylozoo.core.network.sdnetwork.isomorphism phylozoo.core.network.sdnetwork.sd_phynetwork phylozoo.core.network.sdnetwork.transformations phylozoo.core.primitives phylozoo.core.primitives.circular_ordering phylozoo.core.primitives.d_multigraph phylozoo.core.primitives.d_multigraph.base phylozoo.core.primitives.d_multigraph.conversions phylozoo.core.primitives.d_multigraph.features phylozoo.core.primitives.d_multigraph.io phylozoo.core.primitives.d_multigraph.isomorphism phylozoo.core.primitives.d_multigraph.transformations phylozoo.core.primitives.m_multigraph phylozoo.core.primitives.m_multigraph.base phylozoo.core.primitives.m_multigraph.conversions phylozoo.core.primitives.m_multigraph.features phylozoo.core.primitives.m_multigraph.io phylozoo.core.primitives.m_multigraph.isomorphism phylozoo.core.primitives.m_multigraph.transformations phylozoo.core.primitives.partition phylozoo.core.quartet phylozoo.core.quartet.base phylozoo.core.quartet.qdistance phylozoo.core.quartet.qprofile phylozoo.core.quartet.qprofileset phylozoo.core.sequence phylozoo.core.sequence.base phylozoo.core.sequence.bootstrap phylozoo.core.sequence.distances phylozoo.core.sequence.io phylozoo.core.split phylozoo.core.split.algorithms phylozoo.core.split.base phylozoo.core.split.classifications phylozoo.core.split.io phylozoo.core.split.splitsystem phylozoo.core.split.weighted_splitsystem phylozoo.core.triplet phylozoo.core.triplet.base phylozoo.core.triplet.tprofile phylozoo.core.triplet.tprofileset phylozoo.utils phylozoo.utils.exceptions phylozoo.utils.exceptions.algorithm phylozoo.utils.exceptions.base phylozoo.utils.exceptions.general phylozoo.utils.exceptions.generator phylozoo.utils.exceptions.io phylozoo.utils.exceptions.network phylozoo.utils.exceptions.utils phylozoo.utils.exceptions.visualization phylozoo.utils.exceptions.warning phylozoo.utils.io phylozoo.utils.io.file_ops phylozoo.utils.io.format_utils phylozoo.utils.io.format_utils.nexus phylozoo.utils.io.format_utils.phylip phylozoo.utils.io.mixin phylozoo.utils.io.registry phylozoo.utils.parallel phylozoo.utils.validation phylozoo.viz phylozoo.viz.d_multigraph phylozoo.viz.d_multigraph.style phylozoo.viz.dnetwork phylozoo.viz.dnetwork.style phylozoo.viz.m_multigraph phylozoo.viz.m_multigraph.style phylozoo.viz.sdnetwork phylozoo.viz.sdnetwork.style MSA (class in phylozoo.core.sequence.base) multidigraph_to_directedmultigraph() (in module phylozoo.core.primitives.d_multigraph.conversions) multidigraph_to_mixedmultigraph() (in module phylozoo.core.primitives.m_multigraph.conversions) multigraph_to_mixedmultigraph() (in module phylozoo.core.primitives.m_multigraph.conversions) MULTIPROCESSING (phylozoo.utils.parallel.ParallelBackend attribute) MultiprocessingExecutor (class in phylozoo.utils.parallel) N neighbors() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) nexus_header() (in module phylozoo.utils.io.format_utils.nexus) no_validation() (in module phylozoo.utils.validation) node (phylozoo.core.network.dnetwork.generator.side.NodeSide attribute) (phylozoo.core.network.sdnetwork.generator.side.BidirectedEdgeSide attribute) node_color (phylozoo.viz.d_multigraph.style.BaseStyle attribute) node_edge_color (phylozoo.viz.d_multigraph.style.BaseStyle attribute) node_edge_width (phylozoo.viz.d_multigraph.style.BaseStyle attribute) node_size (phylozoo.viz.d_multigraph.style.BaseStyle attribute) nodes (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph property) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph property) nodes_iter() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) NodeSide (class in phylozoo.core.network.dnetwork.generator.side) non_parallel_directed_edge_sides (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) non_parallel_edge_sides (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) normalize_undirected_edge() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph class method) np_array (phylozoo.core.distance.base.DistanceMatrix property) num_taxa (phylozoo.core.sequence.base.MSA property) number_of_connected_components() (in module phylozoo.core.primitives.d_multigraph.features) (in module phylozoo.core.primitives.m_multigraph.features) number_of_edges() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) number_of_nodes() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) O omnians() (in module phylozoo.core.network.dnetwork.features) (in module phylozoo.core.network.sdnetwork.features) order (phylozoo.core.primitives.circular_ordering.CircularOrdering property) orient_away_from_vertex() (in module phylozoo.core.primitives.m_multigraph.transformations) outdegree() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) outgroup (phylozoo.core.triplet.base.Triplet property) P parallel_directed_edge_sides (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) parallel_edge_sides (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) ParallelBackend (class in phylozoo.utils.parallel) ParallelConfig (class in phylozoo.utils.parallel) ParallelExecutor (class in phylozoo.utils.parallel) parents() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) parse_nexus() (in module phylozoo.utils.io.format_utils.nexus) parse_phylip_matrix() (in module phylozoo.utils.io.format_utils.phylip) Partition (class in phylozoo.core.primitives.partition) partition_from_blob() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) parts (phylozoo.core.primitives.partition.Partition property) phylozoo.core module phylozoo.core.distance module phylozoo.core.distance.base module phylozoo.core.distance.classifications module phylozoo.core.distance.decomposition module phylozoo.core.distance.io module phylozoo.core.network module phylozoo.core.network.dnetwork module phylozoo.core.network.dnetwork.base module phylozoo.core.network.dnetwork.classifications module phylozoo.core.network.dnetwork.conversions module phylozoo.core.network.dnetwork.derivations module phylozoo.core.network.dnetwork.features module phylozoo.core.network.dnetwork.generator module phylozoo.core.network.dnetwork.generator.attachment module phylozoo.core.network.dnetwork.generator.base module phylozoo.core.network.dnetwork.generator.construction module phylozoo.core.network.dnetwork.generator.side module phylozoo.core.network.dnetwork.io module phylozoo.core.network.dnetwork.isomorphism module phylozoo.core.network.dnetwork.transformations module phylozoo.core.network.sdnetwork module phylozoo.core.network.sdnetwork.base module phylozoo.core.network.sdnetwork.classifications module phylozoo.core.network.sdnetwork.conversions module phylozoo.core.network.sdnetwork.derivations module phylozoo.core.network.sdnetwork.features module phylozoo.core.network.sdnetwork.generator module phylozoo.core.network.sdnetwork.generator.attachment module phylozoo.core.network.sdnetwork.generator.base module phylozoo.core.network.sdnetwork.generator.construction module phylozoo.core.network.sdnetwork.generator.side module phylozoo.core.network.sdnetwork.io module phylozoo.core.network.sdnetwork.isomorphism module phylozoo.core.network.sdnetwork.sd_phynetwork module phylozoo.core.network.sdnetwork.transformations module phylozoo.core.primitives module phylozoo.core.primitives.circular_ordering module phylozoo.core.primitives.d_multigraph module phylozoo.core.primitives.d_multigraph.base module phylozoo.core.primitives.d_multigraph.conversions module phylozoo.core.primitives.d_multigraph.features module phylozoo.core.primitives.d_multigraph.io module phylozoo.core.primitives.d_multigraph.isomorphism module phylozoo.core.primitives.d_multigraph.transformations module phylozoo.core.primitives.m_multigraph module phylozoo.core.primitives.m_multigraph.base module phylozoo.core.primitives.m_multigraph.conversions module phylozoo.core.primitives.m_multigraph.features module phylozoo.core.primitives.m_multigraph.io module phylozoo.core.primitives.m_multigraph.isomorphism module phylozoo.core.primitives.m_multigraph.transformations module phylozoo.core.primitives.partition module phylozoo.core.quartet module phylozoo.core.quartet.base module phylozoo.core.quartet.qdistance module phylozoo.core.quartet.qprofile module phylozoo.core.quartet.qprofileset module phylozoo.core.sequence module phylozoo.core.sequence.base module phylozoo.core.sequence.bootstrap module phylozoo.core.sequence.distances module phylozoo.core.sequence.io module phylozoo.core.split module phylozoo.core.split.algorithms module phylozoo.core.split.base module phylozoo.core.split.classifications module phylozoo.core.split.io module phylozoo.core.split.splitsystem module phylozoo.core.split.weighted_splitsystem module phylozoo.core.triplet module phylozoo.core.triplet.base module phylozoo.core.triplet.tprofile module phylozoo.core.triplet.tprofileset module phylozoo.utils module phylozoo.utils.exceptions module phylozoo.utils.exceptions.algorithm module phylozoo.utils.exceptions.base module phylozoo.utils.exceptions.general module phylozoo.utils.exceptions.generator module phylozoo.utils.exceptions.io module phylozoo.utils.exceptions.network module phylozoo.utils.exceptions.utils module phylozoo.utils.exceptions.visualization module phylozoo.utils.exceptions.warning module phylozoo.utils.io module phylozoo.utils.io.file_ops module phylozoo.utils.io.format_utils module phylozoo.utils.io.format_utils.nexus module phylozoo.utils.io.format_utils.phylip module phylozoo.utils.io.mixin module phylozoo.utils.io.registry module phylozoo.utils.parallel module phylozoo.utils.validation module phylozoo.viz module phylozoo.viz.d_multigraph module phylozoo.viz.d_multigraph.style module phylozoo.viz.dnetwork module phylozoo.viz.dnetwork.style module phylozoo.viz.m_multigraph module phylozoo.viz.m_multigraph.style module phylozoo.viz.sdnetwork module phylozoo.viz.sdnetwork.style module PhyloZooAlgorithmError PhyloZooAttributeError PhyloZooBackendError PhyloZooEmptyNetworkWarning PhyloZooError PhyloZooFormatError PhyloZooGeneratorDegreeError PhyloZooGeneratorError PhyloZooGeneratorStructureError PhyloZooIdentifierWarning PhyloZooImportError PhyloZooIOError PhyloZooLayoutError PhyloZooNetworkAttributeError PhyloZooNetworkDegreeError PhyloZooNetworkError PhyloZooNetworkStructureError PhyloZooNotImplementedError PhyloZooParseError PhyloZooRuntimeError PhyloZooSingleNodeNetworkWarning PhyloZooStateError PhyloZooTypeError PhyloZooValueError PhyloZooVisualizationError PhyloZooWarning plot() (in module phylozoo.viz) plot_dmgraph() (in module phylozoo.viz.d_multigraph) plot_dnetwork() (in module phylozoo.viz.dnetwork) plot_mmgraph() (in module phylozoo.viz.m_multigraph) plot_sdnetwork() (in module phylozoo.viz.sdnetwork) predecessors() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) profiles (phylozoo.core.quartet.qprofileset.QuartetProfileSet property) (phylozoo.core.triplet.tprofileset.TripletProfileSet property) Q Quartet (class in phylozoo.core.quartet.base) quartet_distance() (in module phylozoo.core.quartet.qdistance) QuartetProfile (class in phylozoo.core.quartet.qprofile) QuartetProfileSet (class in phylozoo.core.quartet.qprofileset) quartets (phylozoo.core.quartet.qprofile.QuartetProfile property) quartets_from_splitsystem() (in module phylozoo.core.split.algorithms) R read_file_safely() (in module phylozoo.utils.io.file_ops) register() (phylozoo.utils.io.registry.FormatRegistry class method) remove_directed_edge() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) remove_directed_edges_from() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) remove_edge() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) remove_edges_from() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) remove_node() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) remove_nodes_from() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) representative_orderings() (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) representative_partitions() (phylozoo.core.primitives.partition.Partition method) reticulation_number() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) root_at_outgroup() (in module phylozoo.core.network.sdnetwork.derivations) root_locations() (in module phylozoo.core.network.sdnetwork.features) root_node (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) S satisfies_triangle_inequality() (in module phylozoo.core.distance.classifications) save() (phylozoo.utils.io.mixin.IOMixin method) SDNetStyle (class in phylozoo.viz.sdnetwork.style) sdnetwork_from_graph() (in module phylozoo.core.network.sdnetwork.conversions) SemiDirectedGenerator (class in phylozoo.core.network.sdnetwork.generator.base) SemiDirectedPhyNetwork (class in phylozoo.core.network.sdnetwork.sd_phynetwork) sequence_length (phylozoo.core.sequence.base.MSA property) SEQUENTIAL (phylozoo.utils.parallel.ParallelBackend attribute) SequentialExecutor (class in phylozoo.utils.parallel) set1 (phylozoo.core.split.base.Split attribute) set2 (phylozoo.core.split.base.Split attribute) set_graph_attribute() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) setorder (phylozoo.core.primitives.circular_ordering.CircularSetOrdering property) Side (class in phylozoo.core.network.dnetwork.generator.side) sides (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator property) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) size() (phylozoo.core.primitives.partition.Partition method) source_components() (in module phylozoo.core.primitives.m_multigraph.features) Split (class in phylozoo.core.split.base) split (phylozoo.core.quartet.base.Quartet property) (phylozoo.core.quartet.qprofile.QuartetProfile property) (phylozoo.core.triplet.base.Triplet property) (phylozoo.core.triplet.tprofile.TripletProfile property) split_decomposition() (in module phylozoo.core.distance.decomposition) split_from_cutedge() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) splits (phylozoo.core.split.splitsystem.SplitSystem property) SplitSystem (class in phylozoo.core.split.splitsystem) starmap() (phylozoo.utils.parallel.MultiprocessingExecutor method) (phylozoo.utils.parallel.ParallelExecutor method) (phylozoo.utils.parallel.SequentialExecutor method) (phylozoo.utils.parallel.ThreadingExecutor method) subgraph() (in module phylozoo.core.primitives.d_multigraph.transformations) (in module phylozoo.core.primitives.m_multigraph.transformations) subnetwork() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) suborderings() (phylozoo.core.primitives.circular_ordering.CircularOrdering method) (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) subpartitions() (phylozoo.core.primitives.partition.Partition method) successors() (phylozoo.core.primitives.d_multigraph.base.DirectedMultiGraph method) suppress_2_blobs() (in module phylozoo.core.network.dnetwork.transformations) (in module phylozoo.core.network.sdnetwork.transformations) suppress_degree2_node() (in module phylozoo.core.primitives.d_multigraph.transformations) (in module phylozoo.core.primitives.m_multigraph.transformations) T taxa (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) (phylozoo.core.quartet.base.Quartet property) (phylozoo.core.quartet.qprofile.QuartetProfile property) (phylozoo.core.quartet.qprofileset.QuartetProfileSet property) (phylozoo.core.sequence.base.MSA property) (phylozoo.core.triplet.base.Triplet property) (phylozoo.core.triplet.tprofile.TripletProfile property) (phylozoo.core.triplet.tprofileset.TripletProfileSet property) taxa_order (phylozoo.core.sequence.base.MSA property) THREADING (phylozoo.utils.parallel.ParallelBackend attribute) ThreadingExecutor (class in phylozoo.utils.parallel) to_circular_ordering() (phylozoo.core.primitives.circular_ordering.CircularSetOrdering method) to_circular_setordering() (phylozoo.core.primitives.circular_ordering.CircularOrdering method) to_csv() (in module phylozoo.core.distance.io) to_d_network() (in module phylozoo.core.network.sdnetwork.derivations) to_dot() (in module phylozoo.core.network.dnetwork.io) (in module phylozoo.core.primitives.d_multigraph.io) to_edgelist() (in module phylozoo.core.primitives.d_multigraph.io) to_enewick() (in module phylozoo.core.network.dnetwork.io) (in module phylozoo.core.network.sdnetwork.io) to_fasta() (in module phylozoo.core.sequence.io) to_lsa_network() (in module phylozoo.core.network.dnetwork.transformations) to_network() (phylozoo.core.quartet.base.Quartet method) (phylozoo.core.triplet.base.Triplet method) to_nexus() (in module phylozoo.core.distance.io) (in module phylozoo.core.sequence.io) to_nexus_split_system() (in module phylozoo.core.split.io) to_nexus_weighted_split_system() (in module phylozoo.core.split.io) to_phylip() (in module phylozoo.core.distance.io) to_phylozoo_dot() (in module phylozoo.core.network.sdnetwork.io) (in module phylozoo.core.primitives.m_multigraph.io) to_sd_network() (in module phylozoo.core.network.dnetwork.derivations) to_string() (phylozoo.utils.io.mixin.IOMixin method) to_weightedsplitsystem() (in module phylozoo.core.split.weighted_splitsystem) total_weight (phylozoo.core.split.weighted_splitsystem.WeightedSplitSystem property) tree_edges (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) tree_from_splitsystem() (in module phylozoo.core.split.algorithms) tree_nodes (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork property) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork property) tree_of_blobs() (in module phylozoo.core.network.dnetwork.derivations) (in module phylozoo.core.network.sdnetwork.derivations) Triplet (class in phylozoo.core.triplet.base) TripletProfile (class in phylozoo.core.triplet.tprofile) TripletProfileSet (class in phylozoo.core.triplet.tprofileset) triplets (phylozoo.core.triplet.tprofile.TripletProfile property) U u (phylozoo.core.network.dnetwork.generator.side.DirEdgeSide attribute) (phylozoo.core.network.sdnetwork.generator.side.UndirEdgeSide attribute) undirected_degree() (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) undirected_edge_sides (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator property) undirected_edges (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph property) undirected_edges_iter() (phylozoo.core.primitives.m_multigraph.base.MixedMultiGraph method) UndirEdgeSide (class in phylozoo.core.network.sdnetwork.generator.side) updown_path_vertices() (in module phylozoo.core.primitives.m_multigraph.features) V v (phylozoo.core.network.dnetwork.generator.side.DirEdgeSide attribute) (phylozoo.core.network.sdnetwork.generator.side.UndirEdgeSide attribute) validate() (phylozoo.core.network.dnetwork.base.DirectedPhyNetwork method) (phylozoo.core.network.dnetwork.generator.base.DirectedGenerator method) (phylozoo.core.network.sdnetwork.base.MixedPhyNetwork method) (phylozoo.core.network.sdnetwork.generator.base.SemiDirectedGenerator method) (phylozoo.core.network.sdnetwork.sd_phynetwork.SemiDirectedPhyNetwork method) validation_aware() (in module phylozoo.utils.validation) vertex_level() (in module phylozoo.core.network.dnetwork.classifications) (in module phylozoo.core.network.sdnetwork.classifications) W warn_on_keyword() (in module phylozoo.utils.exceptions.utils) warn_on_none_value() (in module phylozoo.utils.exceptions.utils) WeightedSplitSystem (class in phylozoo.core.split.weighted_splitsystem) weights (phylozoo.core.split.weighted_splitsystem.WeightedSplitSystem property) with_labels (phylozoo.viz.d_multigraph.style.BaseStyle attribute) write_block() (in module phylozoo.utils.io.format_utils.nexus) write_file_safely() (in module phylozoo.utils.io.file_ops) write_phylip_matrix() (in module phylozoo.utils.io.format_utils.phylip) write_taxa_block() (in module phylozoo.utils.io.format_utils.nexus)
