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# Using a protein model

We use apps to load unaligned DNA sequences and to translate them into amino acids.

## 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 provenance

The parameters used to construct the alignment, including the guide tree and substitution model, are record in the alignment `info` attribute.

The file from which the alignment was derived (the provenance) is on the `.source` attribute.