Tutorials¶
Note
See Data Files Used in the Documentation for data the files used.
Data manipulation¶
General data analysis¶
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
- Perform a coevolutionary analysis on biological sequence alignments
- Analysis of rate heterogeneity
- Evaluate process heterogeneity using a Hidden Markov Model