Welcome to popai’s documentation!

Contents:

• Installing with pip
• Input Data
  • Configuration File
  • Empirical Data
    • Alignments
    • VCF
    • Pop File
  • Model Building Information
    • Species Tree
    • Migration Matrix
• An Explanation of the Demographic Models
  • Demographic models in species delimitation
  • Default demographic models in popai
• User-specified demographic models
  • Configuration File
  • Models Folder
  • Model Files
    • Populations
    • Events
  • Models with different numbers of pouplations/species
  • Plotting user-specified models
  • Running popai with user-specified models
  • Examples
• Tutorial 1a: Running popai through the command line
  • Step 1: Install popai
  • Step 2: Prepare Input
  • Step 3: Processing Empirical data
  • Step 4: Simulate data
  • Step 5: Train networks
  • Step 6: Apply networks
• Tutorial 1b: Processing data from a VCF
  • Step 1: Prepare Input
  • Step 2: Proceed with steps 3-6 of tutorial 1A.
• Tutorial 2: Multiple population trees.
  • Step 1: Prepare Input
  • Step 2: Processing Empirical data
  • Step 3: Simulate data
  • Step 4: Train networks
  • Step 5: Apply networks
• Tutorial 3: User-specified models
  • Step 1: Prepare Input
  • Step 2: Processing Empirical data
  • Step 3: Simulate data
  • Step 4: Train networks
  • Step 5: Apply networks

Indices and tables

• Index

• Module Index

• Search Page