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  • Tutorials
  • API Reference
  • Development
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Contents:

  • Introduction
  • Installation
  • Core Module
    • Overview
    • Multiple Sequence Alignments
    • Pairwise Distances
    • Splits
      • Overview
      • Splits
      • Split Systems
    • Quartets
      • Overview
      • Quartets
      • Quartet Profiles
      • Quartet Profile Sets
    • Networks
      • Overview
      • Directed Networks
        • Overview
        • Directed Network (Class)
        • Directed Network (Advanced Features)
        • Directed Generator
      • Semi-Directed Networks
        • Overview
        • Semi-Directed Network (Class)
        • Semi-Directed Network (Advanced Features)
        • Semi-Directed Generator
    • Primitives
      • Overview
      • Partitions
      • Circular Orderings
      • Directed Multi-Graphs
      • Mixed Multi-Graphs
  • Visualization Module
    • Overview
    • Plotting
    • Styling
  • Utilities Module
    • Overview
    • Input/Output (I/O)
      • Overview
      • I/O Operations
      • File Formats
        • NEXUS
        • PHYLIP
        • eNewick
        • DOT
        • FASTA
        • CSV
        • Edge list
      • Registering a New Format
    • Exceptions
    • Validation
  • Bibliography
  • Manual

Manual#

This manual provides comprehensive guides for using PhyloZoo. For exact specifics of each function and class, see the API Reference.

Contents:

  • Introduction
    • What is PhyloZoo?
    • Package Structure
    • Design Philosophy
    • Getting Started
  • Installation
    • Installing PhyloZoo
      • Requirements
    • Verifying Installation
    • Building Documentation
    • Troubleshooting
  • Core Module
    • Overview
      • Submodules
      • See Also
    • Multiple Sequence Alignments
      • Working with Multiple Sequence Alignments
      • Bootstrap Resampling
      • Distance Computation
      • See Also
    • Pairwise Distances
      • Working with Distance Matrices
      • Classification Functions
      • Traveling Salesman Problem (TSP)
      • See Also
    • Splits
      • Overview
      • Splits
      • Split Systems
    • Quartets
      • Overview
      • Quartets
      • Quartet Profiles
      • Quartet Profile Sets
    • Networks
      • Overview
      • Directed Networks
      • Semi-Directed Networks
    • Primitives
      • Overview
      • Partitions
      • Circular Orderings
      • Directed Multi-Graphs
      • Mixed Multi-Graphs
  • Visualization Module
    • Overview
      • See Also
    • Plotting
      • How to Plot
      • Layouts
      • Saving a Figure
      • See Also
    • Styling
      • Using Styles
      • Styling Parameters
      • Example
      • See Also
  • Utilities Module
    • Overview
      • Submodules
      • See Also
    • Input/Output (I/O)
      • Overview
      • I/O Operations
      • File Formats
      • Registering a New Format
    • Exceptions
      • Errors
      • Warnings
      • See Also
    • Validation
      • What is validation?
      • Which classes are validation-aware?
      • Disabling validation
      • Using the decorator for your own classes
      • See Also
  • Bibliography

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