Programs and Applications

• SumTrees: Phylogenetic Tree Summarization and Annotation
  • Introduction
  • Where to Find the Package
  • How to Install the Package
  • Checking the Installation
  • How to Use the Program
  • Quick Recipes
    • Summarization of Posterior Probabilities of Clades with a Consensus Tree
    • Summarization of Posterior Probabilities of Clades with a Maximum Clade Credibility Tree (MCCT)
    • Non-parametric Bootstrap Support of a Model Tree
    • Set Node Ages of Target or Summary Tree(s) to Mean/Median Node Age of Input Trees
    • Running in Parallel Mode
  • Primers and Examples
  • Specifying and Customization of the Summarization Target
    • Specifying a Summarization Topology Type
      • Majority-Rule Consensus Topology
      • Maximum Clade Credibility Topology
    • Specifying a Custom Topology or Set of Topologies
    • Collapsing Clades/Edges/Splits Below a Minimum Support Frequency Threshold
  • Summarizing Edge Lengths
  • Summarizing Rooted and Ultrametric Trees
    • Forcing Trees to be Treated as Rooted
    • Summarizing Node Ages
    • Setting the Node Ages of the Summary Trees
    • Rooting the Target Topology
  • Assigning the Ages of Non-Contemporaneous Tips (“Tip-Dating”)
  • Parallelizing SumTrees
    • Basics
    • Parallelization Strategy: Deciding on the Number of Processes
    • Running Parallel-Mode SumTrees in a Parallel Environment on a High-Performance Computing (HPC) Cluster
  • Improving Performance
  • Troubleshooting
    • Prerequisites
    • My Computer Does Not Know What a Python Is
  • Manual Installation
  • Repository Access
  • Bugs, Suggestions, Comments, etc.
  • How to Cite this Program
  • Copyright, License, and Warranty
  • Acknowledgments