Introduction | Use examples | Convergence and Convergence Approximations | Visual Examples | Reproducibility | Workflow Requirements | Steps in the Workflow | References

A first example | Model parameters | Initial methylation state distribution | DNA methylation evolution processes | Island-wide events (IWEs) | Single-site events (SSEs) | Simulation Setup | Structural distribution of CpG sites | Parameter values | Simulation of DNA Methylation Data | Simulation of Initial Data | Exploration of Initial Data | Simulation of Data Evolution | References

Introduction | Frequency of Methylation States per Genomic Structure Type | Global Mean | Mean SD of Observed Frequencies per Structure Type at Tree Tips | Mean Correlation of a Central Segment of Methylation States per Genomic Structure Type | Comparison of tree tips | Mean Frequency of Methylation State Changes at Single Sites per Structure Type | Fitch Parsimony Estimate for Minimum Global Methylation State Changes at CpG Islands | Mean Number of Significant Methylation Frequency Changes per Island and Cherry | Mean Number of Significant Methylation Frequency Changes per Island Across All Tree Tips | References