Tutorials

Data manipulation

Title
Map protein alignment gaps to DNA alignment gaps

General data analysis

Title
Estimating periodic signals

Modelling Evolution

Title
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

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

Utilities

Title
Parallel computations