Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y | Z

_

__add__() (dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
__contains__() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
__copy__() (dendropy.datamodel.basemodel.Annotable method)
__delattr__ (dendropy.datamodel.basemodel.Annotable attribute)
(dendropy.datamodel.basemodel.Annotation attribute)
(dendropy.datamodel.basemodel.AnnotationSet attribute)
(dendropy.datamodel.basemodel.DataObject attribute)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
(dendropy.datamodel.datasetmodel.DataSet attribute)
(dendropy.datamodel.treecollectionmodel.TreeList attribute)
(dendropy.datamodel.treemodel.Bipartition attribute)
(dendropy.datamodel.treemodel.Edge attribute)
(dendropy.datamodel.treemodel.Node attribute)
(dendropy.datamodel.treemodel.Tree attribute)
__delattr__() (dendropy.utility.bibtex.BibTexEntry method)
__delitem__() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
__format__() (dendropy.datamodel.basemodel.Annotable method)
(dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.basemodel.DataObject method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Bipartition method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
(dendropy.utility.bibtex.BibTexEntry method)
__getattr__() (dendropy.utility.bibtex.BibTexEntry method)
__getattribute__ (dendropy.datamodel.basemodel.Annotable attribute)
(dendropy.datamodel.basemodel.Annotation attribute)
(dendropy.datamodel.basemodel.AnnotationSet attribute)
(dendropy.datamodel.basemodel.DataObject attribute)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
(dendropy.datamodel.datasetmodel.DataSet attribute)
(dendropy.datamodel.treecollectionmodel.TreeList attribute)
(dendropy.datamodel.treemodel.Bipartition attribute)
(dendropy.datamodel.treemodel.Edge attribute)
(dendropy.datamodel.treemodel.Node attribute)
(dendropy.datamodel.treemodel.Tree attribute)
(dendropy.utility.bibtex.BibTexEntry attribute)
__getitem__() (dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charstatemodel.StateAlphabet method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
(dendropy.datamodel.treecollectionmodel.SplitDistribution method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
__hash__ (dendropy.datamodel.basemodel.Annotable attribute)
(dendropy.datamodel.basemodel.DataObject attribute)
(dendropy.utility.bibtex.BibTexEntry attribute)
__iadd__() (dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
__iter__() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charstatemodel.StateAlphabet method)
(dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treemodel.Tree method)
__len__() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charstatemodel.StateAlphabet method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
__reduce__() (dendropy.datamodel.basemodel.Annotable method)
(dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.basemodel.DataObject method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Bipartition method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
(dendropy.utility.bibtex.BibTexEntry method)
__reduce_ex__() (dendropy.datamodel.basemodel.Annotable method)
(dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.basemodel.DataObject method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Bipartition method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
(dendropy.utility.bibtex.BibTexEntry method)
__repr__ (dendropy.datamodel.basemodel.Annotable attribute)
(dendropy.datamodel.basemodel.Annotation attribute)
(dendropy.datamodel.basemodel.DataObject attribute)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
(dendropy.datamodel.datasetmodel.DataSet attribute)
(dendropy.datamodel.treecollectionmodel.TreeList attribute)
(dendropy.datamodel.treemodel.Bipartition attribute)
(dendropy.datamodel.treemodel.Edge attribute)
__repr__() (dendropy.utility.bibtex.BibTexEntry method)
__setattr__ (dendropy.datamodel.basemodel.Annotable attribute)
(dendropy.datamodel.basemodel.Annotation attribute)
(dendropy.datamodel.basemodel.AnnotationSet attribute)
(dendropy.datamodel.basemodel.DataObject attribute)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
(dendropy.datamodel.datasetmodel.DataSet attribute)
(dendropy.datamodel.treecollectionmodel.TreeList attribute)
(dendropy.datamodel.treemodel.Bipartition attribute)
(dendropy.datamodel.treemodel.Edge attribute)
(dendropy.datamodel.treemodel.Node attribute)
(dendropy.datamodel.treemodel.Tree attribute)
__setattr__() (dendropy.utility.bibtex.BibTexEntry method)
__setitem__() (dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
__sizeof__() (dendropy.datamodel.basemodel.Annotable method)
(dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.basemodel.DataObject method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Bipartition method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
(dendropy.utility.bibtex.BibTexEntry method)
__str__ (dendropy.datamodel.basemodel.Annotable attribute)
(dendropy.datamodel.basemodel.DataObject attribute)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
(dendropy.datamodel.datasetmodel.DataSet attribute)
(dendropy.datamodel.treemodel.Edge attribute)
(dendropy.datamodel.treemodel.Node attribute)
__str__() (dendropy.datamodel.taxonmodel.Taxon method)
(dendropy.datamodel.treemodel.Tree method)
(dendropy.utility.bibtex.BibTexEntry method)

A

accession_index() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
add() (dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.datasetmodel.DataSet method)
add_bibtex() (dendropy.datamodel.basemodel.AnnotationSet method)
add_bound_attribute() (dendropy.datamodel.basemodel.AnnotationSet method)
add_char_matrix() (dendropy.datamodel.datasetmodel.DataSet method)
add_character_subset() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
add_child() (dendropy.datamodel.treemodel.Node method)
add_citation() (dendropy.datamodel.basemodel.AnnotationSet method)
add_new() (dendropy.datamodel.basemodel.AnnotationSet method)
add_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
add_taxa() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
add_taxon() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
add_taxon_namespace() (dendropy.datamodel.datasetmodel.DataSet method)
add_taxon_set() (dendropy.datamodel.datasetmodel.DataSet method)
add_tree() (dendropy.datamodel.treecollectionmodel.TreeArray method)
add_tree_list() (dendropy.datamodel.datasetmodel.DataSet method)
add_trees() (dendropy.datamodel.treecollectionmodel.TreeArray method)
adjacent_edges (dendropy.datamodel.treemodel.Edge attribute)
adjacent_nodes() (dendropy.datamodel.treemodel.Node method)
age_order_iter() (dendropy.datamodel.treemodel.Node method)
age_order_node_iter() (dendropy.datamodel.treemodel.Tree method)
ageorder_iter() (dendropy.datamodel.treemodel.Node method)
ageorder_node_iter() (dendropy.datamodel.treemodel.Tree method)
all_taxa_bitmask() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
ambiguous_state_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
ambiguous_symbol_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
ancestor node
ancestor nodes
ancestor_iter() (dendropy.datamodel.treemodel.Node method)
Annotable (class in dendropy.datamodel.basemodel)
Annotation (class in dendropy.datamodel.basemodel)
annotations_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
AnnotationSet (class in dendropy.datamodel.basemodel)
append() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
(dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
apply() (dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
arborescence
as_ascii_plot() (dendropy.datamodel.treemodel.Tree method)
as_bibtex() (dendropy.utility.bibtex.BibTexEntry method)
as_compact_bibtex() (dendropy.utility.bibtex.BibTexEntry method)
as_data_table() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
as_python_source() (dendropy.datamodel.treemodel.Tree method)
as_string() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
as_tree_array() (dendropy.datamodel.treecollectionmodel.TreeList method)
assemblage_membership_definitions_from_csv() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
attach_taxon_namespace() (dendropy.datamodel.datasetmodel.DataSet method)
attach_taxon_set() (dendropy.datamodel.datasetmodel.DataSet method)
average_number_of_pairwise_differences() (in module dendropy.calculate.popgenstat)

B

B1() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treemeasure)
basal
basal bifurcation
basal node
basal trifurcation
BibTexEntry (class in dendropy.utility.bibtex)
bifurcating node
bifurcating tree
bifurcation
binomial_rv() (in module dendropy.calculate.probability)
bipartition
Bipartition (class in dendropy.datamodel.treemodel)
bipartition (dendropy.datamodel.treemodel.Node attribute)
bipartition_encoding_frequencies() (dendropy.datamodel.treecollectionmodel.TreeArray method)
birth_death_tree() (in module dendropy.model.birthdeath)
(in module dendropy.simulate.treesim)
bitmask_as_newick_string() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
bitmask_taxa_list() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
branch
build_edge_taxa_sets() (dendropy.model.reconcile.ContainingTree method)

C

calc_freqs() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
calc_node_ages() (dendropy.datamodel.treemodel.Tree method)
calc_node_root_distances() (dendropy.datamodel.treemodel.Tree method)
calculate_log_product_of_split_supports() (dendropy.datamodel.treecollectionmodel.TreeArray method)
calculate_sum_of_split_supports() (dendropy.datamodel.treecollectionmodel.TreeArray method)
canonical_symbol_state_map (dendropy.datamodel.charstatemodel.StateAlphabet attribute)
cell_iter() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
character_sequence_type (dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
character_type_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
CharacterDataSequence (class in dendropy.datamodel.charmatrixmodel)
CharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
CharacterSubset (class in dendropy.datamodel.charmatrixmodel)
CharacterType (class in dendropy.datamodel.charmatrixmodel)
child node
child_edge_iter() (dendropy.datamodel.treemodel.Node method)
child_edges() (dendropy.datamodel.treemodel.Node method)
child_node_iter() (dendropy.datamodel.treemodel.Node method)
child_nodes() (dendropy.datamodel.treemodel.Node method)
chisq_pdf() (in module dendropy.calculate.probability)
clear() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
(dendropy.model.reconcile.ContainingTree method)
clear_child_nodes() (dendropy.datamodel.treemodel.Node method)
clear_contained_edges() (dendropy.model.reconcile.ContainingTree method)
clone() (dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.basemodel.DataObject method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
coalesce_nodes() (in module dendropy.model.coalescent)
coalescence_intervals() (dendropy.datamodel.treemodel.Tree method)
coerce_values() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
collapse() (dendropy.datamodel.treemodel.Edge method)
collapse_basal_bifurcation() (dendropy.datamodel.treemodel.Tree method)
collapse_clade() (dendropy.datamodel.treemodel.Node method)
collapse_conflicting() (dendropy.datamodel.treemodel.Node method)
collapse_edges_with_less_than_minimum_support() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
collapse_unweighted_edges() (dendropy.datamodel.treemodel.Tree method)
colless_tree_imbalance() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treemeasure)
compile_bipartition() (dendropy.datamodel.treemodel.Bipartition method)
compile_from_tree() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
compile_lookup_mappings() (dendropy.datamodel.charstatemodel.StateAlphabet method)
compile_member_states_lookup_mappings() (dendropy.datamodel.charstatemodel.StateAlphabet method)
compile_split_bitmask() (dendropy.datamodel.treemodel.Bipartition method)
compile_symbol_lookup_mappings() (dendropy.datamodel.charstatemodel.StateAlphabet method)
compile_tree_leafset_bitmask() (dendropy.datamodel.treemodel.Bipartition method)
concatenate() (dendropy.datamodel.charmatrixmodel.CharacterMatrix class method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
concatenate_from_paths() (dendropy.datamodel.charmatrixmodel.CharacterMatrix class method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
concatenate_from_streams() (dendropy.datamodel.charmatrixmodel.CharacterMatrix class method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
configure() (dendropy.datamodel.treecollectionmodel.SplitDistributionSummarizer method)
consensus() (dendropy.datamodel.treecollectionmodel.TreeList method)
consensus_tree() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
(dendropy.datamodel.treecollectionmodel.TreeArray method)
constrained_kingman_tree() (in module dendropy.model.coalescent)
(in module dendropy.simulate.treesim)
contained_coalescent_tree() (in module dendropy.model.coalescent)
(in module dendropy.simulate.treesim)
ContainingTree (class in dendropy.model.reconcile)
ContinuousCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
contrasts_tree() (dendropy.model.continuous.PhylogeneticIndependentConstrasts method)
copy_annotations_from() (dendropy.datamodel.basemodel.Annotable method)
(dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
corrected_substitution_rate() (dendropy.model.discrete.Hky85 method)
count_splits_on_tree() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)

D

DataObject (class in dendropy.datamodel.basemodel)
DataSet (class in dendropy.datamodel.datasetmodel)
deep_coalescences() (dendropy.model.reconcile.ContainingTree method)
deep_copy_annotations_from() (dendropy.datamodel.basemodel.Annotable method)
(dendropy.datamodel.basemodel.Annotation method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
DEFAULT_TREE_TYPE (dendropy.datamodel.treecollectionmodel.TreeList attribute)
dendropy.calculate.phylogeneticdistance (module)
dendropy.calculate.popgenstat (module)
dendropy.calculate.probability (module)
dendropy.calculate.statistics (module)
dendropy.calculate.treecompare (module)
dendropy.calculate.treemeasure (module)
dendropy.calculate.treescore (module)
dendropy.datamodel.basemodel (module)
dendropy.datamodel.charmatrixmodel (module)
dendropy.datamodel.charstatemodel (module)
dendropy.datamodel.taxonmodel (module)
dendropy.datamodel.treecollectionmodel (module)
dendropy.datamodel.treemodel (module)
dendropy.model.birthdeath (module)
dendropy.model.coalescent (module)
dendropy.model.continuous (module)
dendropy.model.discrete (module)
dendropy.model.parsimony (module)
dendropy.model.reconcile (module)
dendropy.model.treeshape (module)
dendropy.simulate.popgensim (module)
dendropy.simulate.treesim (module)
derived_state_matrix() (in module dendropy.calculate.popgenstat)
descendent nodes
description() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.Taxon method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
(dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
destination node
detach_taxon_namespace() (dendropy.datamodel.datasetmodel.DataSet method)
detach_taxon_set() (dendropy.datamodel.datasetmodel.DataSet method)
discard() (dendropy.datamodel.basemodel.AnnotationSet method)
discard_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
discard_taxon_label() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
discrete_birth_death_tree() (in module dendropy.model.birthdeath)
(in module dendropy.simulate.treesim)
discrete_time_to_coalescence() (in module dendropy.model.coalescent)
DiscreteCharacterEvolutionModel (class in dendropy.model.discrete)
DiscreteCharacterEvolver (class in dendropy.model.discrete)
distance() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
distance_from_root() (dendropy.datamodel.treemodel.Node method)
distance_from_tip() (dendropy.datamodel.treemodel.Node method)
distances() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
distinct_taxon_pair_iter() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
DnaCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
drop() (dendropy.datamodel.basemodel.AnnotationSet method)

E

edge
Edge (class in dendropy.datamodel.treemodel)
edge (dendropy.datamodel.treemodel.Node attribute)
edge length
edge weight
edge_length (dendropy.datamodel.treemodel.Node attribute)
edges() (dendropy.datamodel.treemodel.Tree method)
embed_contained_kingman() (dendropy.model.reconcile.ContainingTree method)
embed_tree() (dendropy.model.reconcile.ContainingTree method)
empirical_cdf() (in module dendropy.calculate.statistics)
empirical_hpd() (in module dendropy.calculate.statistics)
encode_bipartitions() (dendropy.datamodel.treemodel.Tree method)
encode_splits() (dendropy.datamodel.treemodel.Tree method)
euclidean_distance() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treecompare)
evolve_continuous_char() (in module dendropy.model.continuous)
evolve_states() (dendropy.model.discrete.DiscreteCharacterEvolver method)
exp_pdf() (in module dendropy.calculate.probability)
expected_tmrca() (in module dendropy.model.coalescent)
export_character_indices() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
export_character_subset() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
extend() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
(dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
extend_char_matrix_with_characters_on_tree() (dendropy.model.discrete.DiscreteCharacterEvolver method)
extend_matrix() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
extend_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
external edge
external node
extract_coalescent_frames() (in module dendropy.model.coalescent)
extract_subtree() (dendropy.datamodel.treemodel.Node method)
extract_tree() (dendropy.datamodel.treemodel.Tree method)
extract_tree_with_taxa() (dendropy.datamodel.treemodel.Tree method)
extract_tree_with_taxa_labels() (dendropy.datamodel.treemodel.Tree method)
extract_tree_without_taxa() (dendropy.datamodel.treemodel.Tree method)
extract_tree_without_taxa_labels() (dendropy.datamodel.treemodel.Tree method)

F

false_positives_and_negatives() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treecompare)
fields (dendropy.utility.bibtex.BibTexEntry attribute)
fields_as_dict() (dendropy.utility.bibtex.BibTexEntry method)
fill() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
fill_taxa() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
filter_leaf_nodes() (dendropy.datamodel.treemodel.Tree method)
find() (dendropy.datamodel.basemodel.AnnotationSet method)
find_missing_bipartitions() (in module dendropy.calculate.treecompare)
find_missing_splits() (dendropy.datamodel.treemodel.Tree method)
find_node() (dendropy.datamodel.treemodel.Tree method)
find_node_for_taxon() (dendropy.datamodel.treemodel.Tree method)
find_node_with_label() (dendropy.datamodel.treemodel.Tree method)
find_node_with_taxon() (dendropy.datamodel.treemodel.Tree method)
find_node_with_taxon_label() (dendropy.datamodel.treemodel.Tree method)
find_nodes() (dendropy.datamodel.treemodel.Tree method)
findall() (dendropy.datamodel.basemodel.AnnotationSet method)
(dendropy.datamodel.taxonmodel.TaxonNamespace method)
FishersExactTest (class in dendropy.calculate.statistics)
fit_edge_lengths() (dendropy.model.reconcile.ContainingTree method)
fit_pure_birth_model() (in module dendropy.model.birthdeath)
fit_pure_birth_model_to_tree() (in module dendropy.model.birthdeath)
fitch_down_pass() (in module dendropy.model.parsimony)
fitch_up_pass() (in module dendropy.model.parsimony)
frequency_of_bipartition() (dendropy.datamodel.treecollectionmodel.TreeList method)
frequency_of_split() (dendropy.datamodel.treecollectionmodel.TreeList method)
from_bipartition_encoding() (dendropy.datamodel.treemodel.Tree class method)
from_csv() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix class method)
from_dict() (dendropy.datamodel.charmatrixmodel.CharacterMatrix class method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
from_split_bitmasks() (dendropy.datamodel.treemodel.Tree class method)
from_tree() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix class method)
full_symbol_state_map (dendropy.datamodel.charstatemodel.StateAlphabet attribute)
fundamental_indexes (dendropy.datamodel.charstatemodel.StateIdentity attribute)
fundamental_indexes_with_gaps_as_missing (dendropy.datamodel.charstatemodel.StateIdentity attribute)
fundamental_state_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
fundamental_states (dendropy.datamodel.charstatemodel.StateIdentity attribute)
fundamental_symbol_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
fundamental_symbols (dendropy.datamodel.charstatemodel.StateIdentity attribute)

G

geometric_rv() (in module dendropy.calculate.probability)
get() (dendropy.datamodel.charmatrixmodel.CharacterMatrix class method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet class method)
(dendropy.datamodel.treecollectionmodel.TreeList class method)
(dendropy.datamodel.treemodel.Tree class method)
get_adjacent_edges() (dendropy.datamodel.treemodel.Edge method)
get_adjacent_nodes() (dendropy.datamodel.treemodel.Node method)
get_canonical_symbol_for_symbol() (dendropy.datamodel.charstatemodel.StateAlphabet method)
get_from_path() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
get_from_stream() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
get_from_string() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
get_from_url() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
get_fundamental_states_for_symbols() (dendropy.datamodel.charstatemodel.StateAlphabet method)
get_incident_edges() (dendropy.datamodel.treemodel.Node method)
get_split_bitmask_and_edge_tuple() (dendropy.datamodel.treecollectionmodel.TreeArray method)
get_states_for_symbols() (dendropy.datamodel.charstatemodel.StateAlphabet method)
get_taxa() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
get_taxa_bitmask() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
get_taxon() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
get_tree_list() (dendropy.datamodel.datasetmodel.DataSet method)
get_value() (dendropy.datamodel.basemodel.AnnotationSet method)

H

has_annotations_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
has_taxa_labels() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
has_taxon_label() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
head node
Hky85 (class in dendropy.model.discrete)
hky85_chars() (in module dendropy.model.discrete)
hypergeometric_pmf() (in module dendropy.calculate.probability)

I

incident edge
incident_edges() (dendropy.datamodel.treemodel.Node method)
index() (dendropy.datamodel.basemodel.AnnotationSet method)
infer_taxa() (dendropy.datamodel.treemodel.Tree method)
InfiniteSitesCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
inorder_edge_iter() (dendropy.datamodel.treemodel.Tree method)
inorder_iter() (dendropy.datamodel.treemodel.Node method)
inorder_node_iter() (dendropy.datamodel.treemodel.Tree method)
insert() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
(dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
insert_child() (dendropy.datamodel.treemodel.Node method)
insert_new_child() (dendropy.datamodel.treemodel.Node method)
internal edge
internal node
internal_edges() (dendropy.datamodel.treemodel.Tree method)
internal_node_ages() (dendropy.datamodel.treemodel.Tree method)
internal_nodes() (dendropy.datamodel.treemodel.Tree method)
invert() (dendropy.datamodel.treemodel.Edge method)
is_compatible_bitmasks() (dendropy.datamodel.treemodel.Bipartition static method)
is_compatible_with() (dendropy.datamodel.treemodel.Bipartition method)
is_compatible_with_bipartition() (dendropy.datamodel.treemodel.Tree method)
is_exact_correspondence() (dendropy.datamodel.charstatemodel.StateIdentity method)
is_fundamental_state (dendropy.datamodel.charstatemodel.StateIdentity attribute)
is_incompatible_with() (dendropy.datamodel.treemodel.Bipartition method)
is_internal() (dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
is_leaf() (dendropy.datamodel.treemodel.Edge method)
(dendropy.datamodel.treemodel.Node method)
is_leafset_nested_within() (dendropy.datamodel.treemodel.Bipartition method)
is_nested_within() (dendropy.datamodel.treemodel.Bipartition method)
is_purine() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
is_purine_transition() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
is_pyrimidine() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
is_pyrimidine_transition() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
is_single_state (dendropy.datamodel.charstatemodel.StateIdentity attribute)
is_transition() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
is_transversion() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
is_trivial() (dendropy.datamodel.treemodel.Bipartition method)
is_trivial_bitmask() (dendropy.datamodel.treemodel.Bipartition static method)
items() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)

J

Jc69 (class in dendropy.model.discrete)

K

keep_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)

L

label_taxon_map() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
labels() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
ladderize() (dendropy.datamodel.treemodel.Tree method)
leaf edge
leaf node
leaf_edge_iter() (dendropy.datamodel.treemodel.Tree method)
leaf_edges() (dendropy.datamodel.treemodel.Tree method)
leaf_iter() (dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
leaf_node_iter() (dendropy.datamodel.treemodel.Tree method)
leaf_nodes() (dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
leafset_as_bitstring() (dendropy.datamodel.treemodel.Bipartition method)
leafset_as_newick_string() (dendropy.datamodel.treemodel.Bipartition method)
leafset_taxa() (dendropy.datamodel.treemodel.Bipartition method)
left_tail_p() (dendropy.calculate.statistics.FishersExactTest method)
length() (dendropy.datamodel.treemodel.Tree method)
level() (dendropy.datamodel.treemodel.Node method)
level_order_edge_iter() (dendropy.datamodel.treemodel.Tree method)
level_order_iter() (dendropy.datamodel.treemodel.Node method)
level_order_node_iter() (dendropy.datamodel.treemodel.Tree method)
levelorder_edge_iter() (dendropy.datamodel.treemodel.Tree method)
levelorder_iter() (dendropy.datamodel.treemodel.Node method)
levelorder_node_iter() (dendropy.datamodel.treemodel.Tree method)
log_probability_of_coalescent_frames() (in module dendropy.model.coalescent)
log_probability_of_coalescent_tree() (in module dendropy.model.coalescent)
log_product_of_split_support_on_tree() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)

M

mason_gamer_kellogg_score() (in module dendropy.calculate.treecompare)
match_ambiguous_state() (dendropy.datamodel.charstatemodel.StateAlphabet method)
match_polymorphic_state() (dendropy.datamodel.charstatemodel.StateAlphabet method)
match_state() (dendropy.datamodel.charstatemodel.StateAlphabet method)
max_distance_from_root() (dendropy.datamodel.treemodel.Tree method)
max_sequence_size (dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
maximum_product_of_split_support_tree() (dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
maximum_sum_of_split_support_tree() (dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
mean_and_population_variance() (in module dendropy.calculate.statistics)
mean_and_sample_variance() (in module dendropy.calculate.statistics)
mean_kingman_tree() (in module dendropy.model.coalescent)
(in module dendropy.simulate.treesim)
mean_nearest_taxon_distance() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
mean_pairwise_distance() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
median() (in module dendropy.calculate.statistics)
member_states (dendropy.datamodel.charstatemodel.StateIdentity attribute)
member_states_str (dendropy.datamodel.charstatemodel.StateIdentity attribute)
migrate_taxon_namespace() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
minmax_leaf_distance_from_root() (dendropy.datamodel.treemodel.Tree method)
mode() (in module dendropy.calculate.statistics)
monophyletic_partition_discordance() (in module dendropy.model.reconcile)
mrca() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
(dendropy.datamodel.treemodel.Tree method)
multistate_state_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
multistate_symbol_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)

N

N_bar() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treemeasure)
new_ambiguous_state() (dendropy.datamodel.charstatemodel.StateAlphabet method)
new_char_matrix() (dendropy.datamodel.datasetmodel.DataSet method)
new_character_subset() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
new_child() (dendropy.datamodel.treemodel.Node method)
new_fundamental_state() (dendropy.datamodel.charstatemodel.StateAlphabet method)
new_multistate() (dendropy.datamodel.charstatemodel.StateAlphabet method)
new_polymorphic_state() (dendropy.datamodel.charstatemodel.StateAlphabet method)
new_sequence() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
new_symbol_synonym() (dendropy.datamodel.charstatemodel.StateAlphabet method)
new_taxa() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
new_taxon() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
new_taxon_namespace() (dendropy.datamodel.datasetmodel.DataSet method)
new_taxon_set() (dendropy.datamodel.datasetmodel.DataSet method)
new_tree_list() (dendropy.datamodel.datasetmodel.DataSet method)
next() (dendropy.datamodel.basemodel.AnnotationSet method)
nj_tree() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
node
Node (class in dendropy.datamodel.treemodel)
node depth
node height
node_ages() (dendropy.datamodel.treemodel.Tree method)
node_factory() (dendropy.datamodel.treemodel.Tree class method)
node_waiting_time_pairs() (in module dendropy.model.coalescent)
nodes() (dendropy.datamodel.treemodel.Tree method)
normalize() (dendropy.datamodel.treemodel.Bipartition method)
normalize_bitmask() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
nucleotide_diversity() (in module dendropy.calculate.popgenstat)
NucleotideCharacterEvolutionModel (class in dendropy.model.discrete)
num_child_nodes() (dendropy.datamodel.treemodel.Node method)
num_deep_coalescences() (dendropy.model.reconcile.ContainingTree method)
num_lineages_at() (dendropy.datamodel.treemodel.Tree method)
num_poisson_events() (in module dendropy.calculate.probability)
num_segregating_sites() (in module dendropy.calculate.popgenstat)

O

operational taxonomic unit
origin node
outer edge
outer node
outgoing edge

P

pack() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
parent node
parent_node (dendropy.datamodel.treemodel.Node attribute)
parse_text() (dendropy.utility.bibtex.BibTexEntry method)
parsimony_score() (in module dendropy.model.parsimony)
path
path length
path weight
path_edge_count() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
patristic_distance() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
(in module dendropy.calculate.treemeasure)
phylogenetic_distance_matrix() (dendropy.datamodel.treemodel.Tree method)
PhylogeneticDistanceMatrix (class in dendropy.calculate.phylogeneticdistance)
PhylogeneticIndependentConstrasts (class in dendropy.model.continuous)
pij() (dendropy.model.discrete.Hky85 method)
pmatrix() (dendropy.model.discrete.DiscreteCharacterEvolutionModel method)
(dendropy.model.discrete.Hky85 method)
poisson_pmf() (in module dendropy.calculate.probability)
poisson_rv() (in module dendropy.calculate.probability)
poll_taxa() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
polymorphic_state_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
polymorphic_symbol_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
pop() (dendropy.datamodel.basemodel.AnnotationSet method)
pop_gen_tree() (in module dendropy.simulate.popgensim)
postorder traversal
postorder_edge_iter() (dendropy.datamodel.treemodel.Tree method)
postorder_internal_edge_iter() (dendropy.datamodel.treemodel.Tree method)
postorder_internal_node_iter() (dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
postorder_iter() (dendropy.datamodel.treemodel.Node method)
postorder_node_iter() (dendropy.datamodel.treemodel.Tree method)
preorder traversal
preorder_edge_iter() (dendropy.datamodel.treemodel.Tree method)
preorder_internal_edge_iter() (dendropy.datamodel.treemodel.Tree method)
preorder_internal_node_iter() (dendropy.datamodel.treemodel.Node method)
(dendropy.datamodel.treemodel.Tree method)
preorder_iter() (dendropy.datamodel.treemodel.Node method)
preorder_node_iter() (dendropy.datamodel.treemodel.Tree method)
print_plot() (dendropy.datamodel.treemodel.Tree method)
probability_of_table() (dendropy.calculate.statistics.FishersExactTest static method)
ProteinCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
prune_leaves_without_taxa() (dendropy.datamodel.treemodel.Tree method)
prune_subtree() (dendropy.datamodel.treemodel.Tree method)
prune_taxa() (dendropy.datamodel.treemodel.Tree method)
prune_taxa_with_labels() (dendropy.datamodel.treemodel.Tree method)
pure_kingman_tree() (in module dendropy.model.coalescent)
(in module dendropy.simulate.treesim)
pure_kingman_tree_shape() (in module dendropy.model.coalescent)
purge_taxon_namespace() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
put() (dendropy.datamodel.treecollectionmodel.TreeList method)
pvector() (dendropy.model.discrete.Hky85 method)
pybus_harvey_gamma() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treemeasure)

Q

qmatrix() (dendropy.model.discrete.Hky85 method)
quantile_5_95() (in module dendropy.calculate.statistics)

R

randomly_assign_taxa() (dendropy.datamodel.treemodel.Tree method)
randomly_reorient() (dendropy.datamodel.treemodel.Tree method)
randomly_rotate() (dendropy.datamodel.treemodel.Tree method)
rank() (in module dendropy.calculate.statistics)
read() (dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeArray method)
(dendropy.datamodel.treecollectionmodel.TreeList method), [1]
read_from_files() (dendropy.datamodel.treecollectionmodel.TreeArray method)
read_from_path() (dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
read_from_stream() (dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
read_from_string() (dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
read_from_url() (dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
rebuild() (dendropy.model.reconcile.ContainingTree method)
reconciliation_discordance() (in module dendropy.model.reconcile)
reconstruct_taxon_namespace() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
reindex_subcomponent_taxa() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
(dendropy.datamodel.treemodel.Tree method)
reindex_taxa() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
reinsert_nodes() (dendropy.datamodel.treemodel.Node method)
remap_to_default_state_alphabet_by_symbol() (dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
remap_to_state_alphabet_by_symbol() (dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
remove() (dendropy.datamodel.basemodel.AnnotationSet method)
remove_child() (dendropy.datamodel.treemodel.Node method)
remove_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
remove_taxon() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
remove_taxon_label() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
replace_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
require_taxon() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
require_value() (dendropy.datamodel.basemodel.AnnotationSet method)
reroot_at_edge() (dendropy.datamodel.treemodel.Tree method)
reroot_at_midpoint() (dendropy.datamodel.treemodel.Tree method)
reroot_at_node() (dendropy.datamodel.treemodel.Tree method)
reseed_at() (dendropy.datamodel.treemodel.Tree method)
resolve_polytomies() (dendropy.datamodel.treemodel.Tree method)
RestrictionSitesCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
retain_taxa() (dendropy.datamodel.treemodel.Tree method)
retain_taxa_with_labels() (dendropy.datamodel.treemodel.Tree method)
reverse() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
reversible_remove_child() (dendropy.datamodel.treemodel.Node method)
right_tail_p() (dendropy.calculate.statistics.FishersExactTest method)
RnaCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
robinson_foulds_distance() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treecompare)
root node
rooted tree

S

sackin_index() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treemeasure)
sample_multinomial() (in module dendropy.calculate.probability)
scale_edges() (dendropy.datamodel.treemodel.Tree method)
schema
seed node
sequence_size (dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)
sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
set_annotations_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
set_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
set_character_type_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
set_child_nodes() (dendropy.datamodel.treemodel.Node method)
set_children() (dendropy.datamodel.treemodel.Node method)
set_edge_lengths_from_node_ages() (dendropy.datamodel.treemodel.Tree method)
set_state_as_attribute() (dendropy.datamodel.charstatemodel.StateAlphabet method)
shuffle_taxa() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
(dendropy.datamodel.treemodel.Tree method)
sibling node
sibling_nodes() (dendropy.datamodel.treemodel.Node method)
simulate_contained_kingman() (dendropy.model.reconcile.ContainingTree method)
simulate_descendant_states() (dendropy.model.discrete.DiscreteCharacterEvolutionModel method)
simulate_discrete_char_dataset() (in module dendropy.model.discrete)
simulate_discrete_chars() (in module dendropy.model.discrete)
sister node
sister_nodes() (dendropy.datamodel.treemodel.Node method)
sort() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
source node
split
split_as_bitstring() (dendropy.datamodel.treemodel.Bipartition method)
split_as_newick_string() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
(dendropy.datamodel.treemodel.Bipartition method)
split_bitmask_set_frequencies() (dendropy.datamodel.treecollectionmodel.TreeArray method)
split_distribution() (dendropy.datamodel.treecollectionmodel.TreeList method)
split_support_iter() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
SplitDistribution (class in dendropy.datamodel.treecollectionmodel)
SplitDistributionSummarizer (class in dendropy.datamodel.treecollectionmodel)
splits_considered() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
StandardCharacterMatrix (class in dendropy.datamodel.charmatrixmodel)
standardized_effect_size_mean_nearest_taxon_distance() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
standardized_effect_size_mean_pairwise_distance() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
star_tree() (in module dendropy.model.treeshape)
(in module dendropy.simulate.treesim)
state_alphabet (dendropy.datamodel.charmatrixmodel.CharacterType attribute)
state_denomination (dendropy.datamodel.charstatemodel.StateIdentity attribute)
state_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
StateAlphabet (class in dendropy.datamodel.charstatemodel)
StateIdentity (class in dendropy.datamodel.charstatemodel)
states (dendropy.datamodel.charstatemodel.StateAlphabet attribute)
stationary_sample() (dendropy.model.discrete.NucleotideCharacterEvolutionModel method)
strip_comments() (dendropy.datamodel.treemodel.Tree method)
subtending edge
subtree
sum_of_distances() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
sum_of_split_support_on_tree() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
summarize() (in module dendropy.calculate.statistics)
summarize_splits_on_tree() (dendropy.datamodel.treecollectionmodel.SplitDistribution method)
suppress_unifurcations() (dendropy.datamodel.treemodel.Tree method)
symbol (dendropy.datamodel.charstatemodel.StateIdentity attribute)
symbol_state_pair_iter() (dendropy.datamodel.charstatemodel.StateAlphabet method)
symbol_synonyms (dendropy.datamodel.charstatemodel.StateIdentity attribute)
symbols (dendropy.datamodel.charstatemodel.StateAlphabet attribute)
symbols_as_list() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
symbols_as_string() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
symmetric_difference() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treecompare)

T

tail node
tajimas_d() (in module dendropy.calculate.popgenstat)
target node
taxa_bipartition() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
taxa_bitmask() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
taxon
Taxon (class in dendropy.datamodel.taxonmodel)
taxon concept
taxon name
taxon namespace
taxon_bitmask() (dendropy.datamodel.taxonmodel.TaxonNamespace method)
taxon_iter() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)
taxon_namespace_scoped_copy() (dendropy.datamodel.basemodel.DataObject method)
taxon_state_sets_map() (dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
TaxonNamespace (class in dendropy.datamodel.taxonmodel)
TaxonNamespaceAssociated (class in dendropy.datamodel.taxonmodel)
terminal edge
terminal node
time_to_coalescence() (in module dendropy.model.coalescent)
tip node
to_outgroup_position() (dendropy.datamodel.treemodel.Tree method)
topologies() (dendropy.datamodel.treecollectionmodel.TreeArray method)
tree
Tree (class in dendropy.datamodel.treemodel)
tree (dendropy.model.continuous.PhylogeneticIndependentConstrasts attribute)
tree_factory() (dendropy.datamodel.treecollectionmodel.TreeList class method)
TreeArray (class in dendropy.datamodel.treecollectionmodel)
TreeList (class in dendropy.datamodel.treecollectionmodel)
treeness() (dendropy.datamodel.treemodel.Tree method)
(in module dendropy.calculate.treemeasure)
two_tail_p() (dendropy.calculate.statistics.FishersExactTest method)

U

unassign_taxa() (dendropy.datamodel.treemodel.Tree method)
unfolded_site_frequency_spectrum() (in module dendropy.calculate.popgenstat)
uniform_pure_birth_tree() (in module dendropy.model.birthdeath)
unifurcating node
unifurcation
unify_taxon_namespaces() (dendropy.datamodel.datasetmodel.DataSet method)
unrooted tree
unweighted path
unweighted_robinson_foulds_distance() (in module dendropy.calculate.treecompare)
update() (dendropy.datamodel.basemodel.AnnotationSet method)
update_bipartitions() (dendropy.datamodel.treemodel.Tree method)
update_sequences() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
update_splits() (dendropy.datamodel.treemodel.Tree method)
update_taxon_namespace() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.taxonmodel.TaxonNamespaceAssociated method)
(dendropy.datamodel.treemodel.Tree method)
upgma_tree() (dendropy.calculate.phylogeneticdistance.PhylogeneticDistanceMatrix method)

V

value_at() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
values() (dendropy.datamodel.charmatrixmodel.CharacterDataSequence method)
(dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
values_as_dict() (dendropy.datamodel.basemodel.AnnotationSet method)
variance_covariance() (in module dendropy.calculate.statistics)
vector_size (dendropy.datamodel.charmatrixmodel.CharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix attribute)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix attribute)

W

wattersons_theta() (in module dendropy.calculate.popgenstat)
weighted path
weighted_choice() (in module dendropy.calculate.probability)
weighted_index_choice() (in module dendropy.calculate.probability)
weighted_robinson_foulds_distance() (in module dendropy.calculate.treecompare)
write() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
write_as_dot() (dendropy.datamodel.treemodel.Tree method)
write_as_mesquite() (dendropy.model.reconcile.ContainingTree method)
write_ascii_plot() (dendropy.datamodel.treemodel.Tree method)
write_to_path() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)
write_to_stream() (dendropy.datamodel.charmatrixmodel.CharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ContinuousCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.InfiniteSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.ProteinCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RestrictionSitesCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.RnaCharacterMatrix method)
(dendropy.datamodel.charmatrixmodel.StandardCharacterMatrix method)
(dendropy.datamodel.datasetmodel.DataSet method)
(dendropy.datamodel.treecollectionmodel.TreeList method)
(dendropy.datamodel.treemodel.Tree method)

Y

yield_from_files() (dendropy.datamodel.treemodel.Tree class method)

Z

z_pmf() (in module dendropy.calculate.probability)