How do I convert an alignment of coding sequences to a protein alignment?
This article describes steps to convert a multiple sequence alignment of coding sequences to a protein alignment. The same steps can be followed for DNA pairwise alignments.
Open or Create a DNA Alignment of Coding Sequences (CDS)
Open an alignment of coding sequences, or create an alignment (see Create a Multiple Sequence Alignment or Create a Pairwise DNA Alignment) of coding sequences.
Sequence the Sequences for Translation
Click Edit → Select All to select all sequences in the alignment, or hold down the command (macOS) or CTRL (Windows/Ubuntu) and click on the names of individual sequences to select or deselect individual sequences.
You can also click within the sequences and drag-select to select just a section of the alignment and/or a subset of the sequences.
If a sequence has a CDS feature, then click the disclosure triangle to see the translation and confirm you select the CDS reading frame.
Create the Protein Alignment
Click Alignments → Convert Selection to a Protein Alignment.
In the dialog that opens:
An example translation of the first sequence is shown. Internal stop codons will likely indicate the wrong genetic code is used for translation, or the wrong frame has been translated.
If required, set the appropriate "Genetic code for translation" using the dropdown menu.
If required, set an alternative reading frame for correct translation.
Click OK to create the new protein alignment.
A protein alignment will be generated by translation using all selected sequences, and alignment using the same alignment algorithm/s as that used to generate the DNA sequence alignment.
To realign the protein alignment using an alternative algorithm see Repeat an Alignment with an Alternative Algorithm, New Parameters or Changed Input.
Save the Protein Alignment
Click File → Save to save the new protein alignment to an appropriate location on your computer.
