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.