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.
Overview¶
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.
- Apply a non-stationary nucleotide model to an alignment with 3 sequences
- Apply a non-stationary nucleotide model to an alignment with a tree
- Specifying a non-stationary model with time-heterogeneous parameters
- Extracting maximum likelihood estimates from a
model_result
- Reconstructing ancestral states
- Applying a discrete-time, non-stationary nucleotide model
- Applying a time-reversible nucleotide model
- Applying GNC, a non-stationary codon model
- Applying a time-reversible codon model
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