The apps

cogent3 comes with pre-defined “apps” which perform single functions that can be configured by the user. Apps are designed to enable usage without requiring detailed understanding of programming and so they can be applied in batch to a large amount of data. In other words, being able to use them as functions without writing loops or conditionals.

Apps can be used by themselves, or added together to define a “composed function” (aka pipeline). Composed functions can be applied to a single, or thousands, of data file(s).

Apps have several key features

  1. trap errors

  2. check the validity of input data

  3. can be used by themselves or combined into a “composed” app

  4. automatically track the relationship between an input data record and its output record


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.

Write your own Apps

You can write your own apps.