Tutorials and Examples

• Introduction
  • For the impatient
• Using p4
  • Using the p4 script
  • Some peculiarities, bugs, and “features”
  • The var object, the global bucket
  • The read() function
  • The dump() function and methods
• Customizing
  • Setting var variables
  • Add your own code
  • Using interactive helpers
  • Using p3rlcompleter
  • Interfacing with your editor
• Alignments and data
  • Alignment, Part, and Data classes
  • Nexus charpartitions
  • Subsetting alignments
  • Nexus standard datatype
  • (Non-parametric) bootstrapping of data
  • Dealing with duplicate sequences
• Trees
  • Tree, Node, and Trees classes
  • Tree pictures and drawings
  • Topology distance
  • Patristic distances
• Models and likelihood
  • Describing models
• Simulating data
• Simulations with reference data
  • The ususal way to simulate data based on a tree and a model
  • PhyloBayes has an unusual way to simulate data — using a tree, model, and reference data
  • An implementation in p4
• Bayesian analysis with MCMC
  • A simple MCMC
  • Proposal probabilities
  • The polytomy proposal
  • Topology constraints
  • Tuning the MCMC
  • Assessing the MCMC run
  • Checkpoints
  • Restarting from checkpoints
  • Output
  • Posterior predictive simulations
• Compositional homogeneity tests
• Model fit tests
• Drawing trees
  • Drawing a tree with TV and BTV
  • Comparing two trees with a GUI
  • Drawing radial phylograms
• To collapse nodes in a tree
• To combine tree supports from two analyses onto one tree
• Making a tree from compositions
• Doing MRP, Matrix representation / parsimony
• Kosiol’s AIS, almost invariant sets
• Assessing partition composition differences
  • Testing whether two unrelated sequences have different compositions
  • Testing whether two related sequences have different compositions
  • Testing whether two related partitions have different compositions
  • Comparing constant with variable sites
  • Comparing autapomorphic sites with other variable sites
  • An example using the Cox et al 2008 data
• Ancestral character state reconstruction