DendroPy Library Reference

Data Model

• dendropy.datamodel.basemodel: Core Infrastructure for Phylogenetic Data Objects
  • The DataObject Class
  • The Annotable Class
  • The Annotation Class
  • The AnnotationSet Class
  • Supporting Classes
• dendropy.datamodel.taxonmodel: Taxonomic Namespace Reference and Management
  • The TaxonNamespace Class
  • The Taxon Class
  • The TaxonNamespaceAssociated Class
• dendropy.datamodel.treemodel: Trees
  • The Tree Class
  • The Node Class
  • The Edge Class
  • The Bipartition Class
  • The AsciiTreePlot Class
• dendropy.datamodel.treecollectionmodel: Collections of Trees
  • The TreeList Class
  • The TreeArray Class
  • The SplitDistribution Class
  • The SplitDistributionSummarizer Class
• dendropy.datamodel.charstatemodel: Character State Identities and Alphabets
  • The StateAlphabet Class
  • The StateIdentity Class
• dendropy.datamodel.charmatrixmodel: Character Sequences and Matrices
  • Character Sequences
  • Character Types
  • Character Subsets
  • Character Matrices
• dendropy.datamodel.datasetmodel: Datasets – Aggregate Collections of Taxon, Character, and Tree Data
  • DataSet
• dendropy.calculate.phylogeneticdistance: Phylogenetic Distance Calculations and Operations
  • The PhylogeneticDistanceMatrix Class

Process Models

• dendropy.model.birthdeath: The Birth-Death and Related Processes
  • birth_death_likelihood
  • birth_death_tree
  • discrete_birth_death_tree
  • fit_pure_birth_model
  • fit_pure_birth_model_to_tree
  • uniform_pure_birth_tree
• dendropy.model.coalescent: The Coalescent
  • coalesce_nodes
  • constrained_kingman_tree
  • contained_coalescent_tree
  • discrete_time_to_coalescence
  • expected_tmrca
  • extract_coalescent_frames
  • log_probability_of_coalescent_frames
  • log_probability_of_coalescent_tree
  • mean_kingman_tree
  • node_waiting_time_pairs
  • pure_kingman_tree
  • pure_kingman_tree_shape
  • time_to_coalescence
• dendropy.model.continuous: Continuous Character Evolution
  • PhylogeneticIndependentContrasts
  • evolve_continuous_char
• dendropy.model.discrete: Discrete Character Evolution
  • DiscreteCharacterEvolutionModel
  • DiscreteCharacterEvolver
  • Hky85
  • Jc69
  • NucleotideCharacterEvolutionModel
  • hky85_chars
  • simulate_discrete_char_dataset
  • simulate_discrete_chars
• dendropy.model.parsimony: The Parsimony Model
  • fitch_down_pass
  • fitch_up_pass
  • parsimony_score
• dendropy.model.protractedspeciation: The Protracted Speciation (Birth-Death) Model
  • expected_duration_of_speciation
  • log_probability_of_duration_of_speciation
  • maximum_probability_duration_of_speciation
  • probability_of_duration_of_speciation
  • The ProtractedSpeciationProcess Class
• dendropy.model.reconcile: Tree-Fitting (Gene/Species, Parasite/Host, etc.)
  • ContainingTree
  • monophyletic_partition_discordance
  • reconciliation_discordance
• dendropy.model.treeshape: Models of Tree Shape
  • star_tree

Calculations, Statistics, and Metrics

• dendropy.calculate.treemeasure: Unary Tree Statistics and Metrics
  • B1
  • N_bar
  • PatristicDistanceMatrix
  • coalescence_ages
  • colless_tree_imbalance
  • divergence_times
  • node_ages
  • node_depths
  • patristic_distance
  • pybus_harvey_gamma
  • sackin_index
  • treeness
• dendropy.calculate.treecompare: Distances and Comparison Between Trees
  • euclidean_distance
  • false_positives_and_negatives
  • find_missing_bipartitions
  • mason_gamer_kellogg_score
  • robinson_foulds_distance
  • symmetric_difference
  • unweighted_robinson_foulds_distance
  • weighted_robinson_foulds_distance
• dendropy.calculate.treescore: Scoring Trees with Reference to Data and a Model
• dendropy.calculate.popgenstat: Population Genetics Statistics
  • average_number_of_pairwise_differences
  • derived_state_matrix
  • nucleotide_diversity
  • num_segregating_sites
  • tajimas_d
  • unfolded_site_frequency_spectrum
  • wattersons_theta
• dendropy.calculate.probability: General Probability
  • binomial_rv
  • chisq_pdf
  • exp_pdf
  • geometric_rv
  • hypergeometric_pmf
  • num_poisson_events
  • poisson_pmf
  • poisson_rv
  • sample_multinomial
  • weighted_choice
  • weighted_index_choice
  • z_pmf
• dendropy.calculate.statistics: General Statistics
  • FishersExactTest
  • empirical_cdf
  • empirical_hpd
  • mean_and_population_variance
  • mean_and_sample_variance
  • median
  • mode
  • quantile_5_95
  • rank
  • summarize
  • variance_covariance

Simulations

• dendropy.simulate.treesim: Unified Namespace Aggregating Functions and Classes for Tree Simulations
  • birth_death_tree
  • constrained_kingman_tree
  • contained_coalescent_tree
  • discrete_birth_death_tree
  • mean_kingman_tree
  • pure_kingman_tree
  • rand_trees
  • star_tree
• dendropy.simulate.popgensim: Population Genetics Simulations
  • pop_gen_tree