Tutorials

Data manipulation

• Map protein alignment gaps to DNA alignment gaps
• Manipulation of Tree Node Objects
• An Example of Conditional Tree Node Modifications

General data analysis

• Estimating periodic signals

Modelling Evolution

• The simplest script
• Performing a relative rate test
• A test of the neutral theory
• Allowing substitution model parameters to differ between branches
• Using codon models
• Use an empirical protein substitution model
• Likelihood analysis of multiple loci
• Simulate an alignment
• Performing a parametric bootstrap
• Analysis of rate heterogeneity
• Evaluate process heterogeneity using a Hidden Markov Model
• Inferring Amino Acid frequencies with a nonstationary model

Phylogenetic Reconstruction

• Calculate pairwise distances between sequences
• Make a neighbor joining tree
• Make a UPGMA cluster
• Phylogenetic reconstruction by least squares

Utilities

• Parallel computations