# 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