The DendroPy Primer

The DendroPy Data Model: Phylogenetic Data Objects

• Introduction to Phylogenetic Data Objects
  • Primary Phylogenetic Data Objects
  • Creating New (Empty) Objects
  • Reading, Writing, and Annotating Phylogenetic Data
• Reading and Writing Phylogenetic Data
  • Creating New Objects From an External Data Source
  • Adding Data to Existing Objects from an External Data Source
  • Writing Out Phylogenetic Data
• Converting Between Data Formats

Working with Taxa: Operational Taxonomic Units and Taxon Namespaces

• Taxon Namespaces and Taxon Management
  • Conceptual Background
  • Management of Shared Taxon Namespaces
  • Managing Taxon Name Mapping Within a Taxon Namespace
• Partitions of Taxon Sets

Working with Trees and Tree Lists

• Trees
  • The Tree Class
  • Reading and Writing Tree Instances
  • Cloning/Copying a Tree
  • Tree Traversal
  • Finding Nodes on Trees
  • Viewing and Displaying Trees
  • Building a Tree Programmatically
• Collections of Trees
  • Collections of Trees: The TreeList Class
  • Efficiently Iterating Over Trees in a File
• Tree Statistics, Metrics, Summarizations, and Other Calculations
  • Native Tree Statistic and Metric Methods
  • Unary Tree Statistics and Metrics
  • Comparing and Summarizing Trees
  • Scoring Trees Under the Coalescent
• Tree Manipulation and Restructuring
  • Rooting, Derooting and Rerooting
  • Pruning Subtrees and Tips
  • Extracting Trees and Subtrees from an Existing Tree
  • Rotating
• Bipartitions
  • Modeling Bipartitions
  • Using Bipartitions
• Tree Simulation and Generation
  • Birth-Death Process Trees
  • Star Trees
  • (Pure Neutral) Coalescent Trees
  • Multispecies Coalescent (“Contained Coalescent” or “Censored Coalescent”) Trees
  • Simulating the Distribution of Number Deep Coalescences Under Different Phylogeographic History Scenarios

Working with Character Data: Sequences and Matrices

• Character Matrices
  • Types of Character Matrices
  • Reading and Writing Character Data
  • Creating a Character Data Matrix from a Dictionary of Strings
  • Taxon Management with Character Matrices
  • Concatenating Multiple Data Matrices
  • Sequence Management
  • Accessing Data
• Phylogenetic Character Analyses
  • Phylogenetic Independent Contrasts (PIC)
• Population Genetic Summary Statistics

Working with Phylogenetic Distances

• Phylogenetic Distance-Based Operations
  • Creating a PhylogeneticDistanceMatrix Object
  • Calculating Patristic Distances and Most-Recent Common Ancestors (MRCA)
  • Generating Distance Trees from a PhylogeneticDistanceMatrix Object
  • Phylogenetic Community Statistics

Working with Data Sets

• Data Sets
  • DataSet Creation and Reading
  • Taxon Management with Data Sets

Working with Metadata Annotations

• Working with Metadata Annotations
  • Overview of the Infrastructure for Metadata Annotation in DendroPy
  • Metadata Annotation Creation
  • Metadata Annotation Access and Manipulation
  • Writing or Saving Metadata

Interoperability with Other Programs, Libraries and Applications

• Working with GenBank Molecular Sequence Databases
  • Quick Start
  • Acquiring Data from GeneBank
  • Accessing GenBank Records
  • Generating Character Matrix Objects from GenBank Data
• Seq-Gen
• PAUP
• RAxML