# Using a protein model

We load the unaligned sequences we will use in our examples and translate them.

## Protein alignment with default settings

The default setting for “protein” is a WG01 model.

## Specify a different distance measure for estimating the guide tree

The distance measures available are percent or paralinear.

Note

An estimated guide tree has its branch lengths scaled so they are consistent with usage in a codon model.

## Alignment settings and file provenance are recorded in the `info` attribute