# Genetic distance calculation

## Fast pairwise distance estimation

For a limited number of evolutionary models a fast implementation is available.

## Computing genetic distances using the `Alignment` object

Abbreviations listed from `available_distances()` can be used as values for the `distance_matrix(calc=<abbreviation>)`.

## Using the distance calculator directly

The distance calculation object can provide more information. For instance, the standard errors.

## Likelihood based pairwise distance estimation

The standard `cogent3` likelihood function can also be used to estimate distances. Because these require numerical optimisation they can be significantly slower than the fast estimation approach above.

The following will use the F81 nucleotide substitution model and perform numerical optimisation.