Contents

• Introduction
• Overview
  • Philosophy
  • Overview of the algorithm
  • Technical capabilities and limitations
  
  
• Installation instructions
  • Windows version
  • Linux version
  
  
• The interface
• Input format
  • Genetic map distances
  • Missing information and unknown phase
  • TDT-data
  
  
• Running TreeLD
  • Create a project
  • Generating trees
  • Analysis of the trees with the peeling algorithm
  • Generating the posterior distribution
  • Testing for the presence of a disease mutation
  • Generating additional trees
  
  
• Additional options
  • Visual analysis of trees
  • Creating tree building scripts
  • Generating tree peeling scripts
  • Exporting images
  
  
• Choosing parameters for the Markov Chain Monte Carlo
  • Choosing burn-in
  • Effect of outliers among the sampled trees
  • Density of focal points
  • Strategy
  
  
• How to cite this program
• Bibliography
• Index