pyslim
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Contents:

  • Introduction
  • Installation
  • Troubleshooting
  • Tutorial
  • Vignette: A spatial simulation
  • Vignette: Following up with more coalescent simulation
  • Metadata
  • Legacy metadata
  • Python API
  • Development
pyslim
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  • Welcome to pyslim’s documentation!
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Welcome to pyslim’s documentation!¶

Contents:

  • Introduction
    • Overview
    • What does SLiM record in the tree sequence?
    • Who and what is in the tree sequence?
    • What else can I find out from the tree sequence?
  • Installation
  • Troubleshooting
  • Tutorial
    • Recapitation
    • Simplification
    • Adding neutral mutations to a SLiM simulation
    • Extracting particular SLiM individuals
    • Reading SLiM metadata
    • Coalescent simulation for SLiM
    • Extracting information about selected mutations
    • Possibly important technical notes
  • Vignette: A spatial simulation
    • Simulation
    • Recapitation and mutation
    • Take a sample of individuals
    • Plotting locations
    • Isolation by distance
    • VCF output
    • More information
    • What about simplification?
  • Vignette: Following up with more coalescent simulation
    • Positive selection
    • Recapitation
    • Continuing the simulation
  • Metadata
    • Converting from SLiM time to tskit time
    • Modifying SLiM metadata
    • Technical details
  • Legacy metadata
  • Python API
    • Additions to the tree sequence
    • Constants
    • Metadata
  • Development
    • Quickstart

Indices and tables¶

  • Index
  • Module Index
  • Search Page
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