The apps

cogent3 comes with pre-defined “apps”. These are capabilities that can be used by themselves, or added together to define a pipeline. Apps that can be combined into a pipeline are called composable.

The progressive_align App

cogent3 has a built-in progressive aligner. This is a tree-based HMM aligner that can use any cogent3 substitution model.

The model App

cogent3 possesses unique capabilities for molecular evolutionary analyses. Of particular significance are our non-stationary model classes and the associated measurement of genetic distance from these. That said, we also implement most of the conventional substitution models. See cogent3.available_models() for a display of the built-in models.

You can use these models either through the general model app, or some task specific apps. Both are described below.

The hypothesis App

Takes two (or more) model instances and performs hypothesis test.

The natsel Apps

These apps all employ codon models to evaluate different types of hypotheses regarding the mode of natural selection.

The user_function Apps

These apps are capable to wrap another user specified function