Usage Examples¶
Data manipulation¶
- Translating DNA into protein
- Advanced sequence handling
- Complete version of manipulating sequence annotations
- Getting the reverse complement
- Map protein alignment gaps to DNA alignment gaps
- Data Manipulation using
Table
- Manipulation of Tree Node Objects
- An Example of Conditional Tree Node Modifications
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