Documentation¶
cogent3 is a software library for genomic biology. It is a comprehensive framework for manipulation of genomic sequence data and for conducting molecular evolutionary analyses. It is distinguished by many unique built-in capabilities. Of particular note are our non-stationary Markov substitution models. These include non-stationary nucleotide, and non-stationary codon models.
Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process.
Plus, the ability to manipulate biological sequences by their annotations.
Click to see an animation showing defining and using sequence annotations.
cogent3 apps
cogent3 comes with pre-defined “apps” that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines.
Cookbook
The cookbook presents short code recipes targeted at specific problems.
Tutorials
The tutorials present code for solving more extensive problems.
API
The API for major cogent3 objects