Cogent3 Usage Examples

A Note on the Computable Documentation

The following examples are all available as standalone text files which can be computed using the Python doctest module.

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

• 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
• Perform a coevolutionary analysis on biological sequence alignments
• Analysis of rate heterogeneity
• Evaluate process heterogeneity using a Hidden Markov Model

Phylogenetic Reconstruction

• Calculate pairwise distances between sequences
• Make a neighbor joining tree
• Make a UPGMA cluster
• Phylogenetic reconstruction by least squares
• Making a phylogenetic tree from a protein sequence alignment