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 click/shift click on the names of individual sequences to select a subset of sequences.
Alternatively, click within the sequences and drag-select to select a section of the alignment and/or a subset of the sequences.
Click Alignments → Convert Selection to a Protein Alignment.
An example translation of the first sequence is shown in the dialog. Internal stop codons, likely indicate the wrong genetic code is used for translation, or the wrong frame has been translated.
Set the "Genetic code for translation" using the dropdown menu.
If required set the reading frame for translation.
Confirm that the sequence is correctly translated and contains no internal stop codons.
Click OK to create an alignment.
The protein alignment will be generated by translation of all 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.