User Guide

The user guide is a set of tutorials for a user to explore various aspects of saegus while simultaneously learning about the powerful infrastructure of simuPOP.

Table of Contents

• Creating a Population From Raw Data
  • Parsing Raw Data
  • Creating and Saving the Population
• Additive Trait Parameterization
  • Preparing the Population
  • Additive Trait
• Expanding A Population According to Structure Matrix
  • Validating the Mating Probabilities
  • Assigning Primary Subpopulations
  • Parent Chooser and Recombination Map
  • Expanding the Population
• Creating Multi-Parental Populations
  • Example Multi-Parental Population
  • Multi-Parental Breeding Protocol
• Collect and Store Data
  • Categories of Data
  • Storing Data in HDF5 Files
  • Very Brief Example HDF5 in R
• Integrated Example: Multiple Generations and Data Storage
  • Creating the Multi-Parental Population
  • Additive Trait
  • Opening the HDF5 File and Declaring Groups
  • Ten Generations of Random Mating
• Using Standalone Tassel for Multi-Locus Trait Mapping
  • Setting up the Population for Analysis
  • Hapmap Formatted Data
  • Population Structure
  • Kinship Matrix
  • Trait
  • TASSEL Config File
  • Running TASSEL Mixed Linear Model
• Visualization in Bokeh
  • Module Imports for Packages Used to Make Plots
  • Simple Bokeh Quad Plot
  • Chromosome Ideogram
  • Distribution Plots