Tutorials

We'd love to see you built upon PYggdrasil. Below, we provide some tutorials to help you get started.

Functional Usage

The tutorials below illustrate how to use PYggdrasil functions for specific tasks.

• Single MCMC Run demonstrates how to run a single MCMC chain.
• Tree Similarities and Visualization demonstrates how to compute distances between two trees and visualize trees.
• Analyzing MCMC Runs demonstrates how to compute distances between MCMC chains and diagnose convergence issues.

Experimental Workflows

We use snakemake to create a sustainable and reproducible workflow for extensive experiments with PYggdrasil. See Workflows for more details.

The tutorials below illustrate snakemake workflows that allow running such fully reproducible experiments using PYggdrasil. From tree and data generation to convergence diagnostics, a pipeline exists.

• Basic Workflow demonstrates a basic workflow for a particular output file.
• Advanced Workflow demonstrates how to run a more advanced workflow.