Figure 9.4:
Options for nucleotide translation alignment
In a translation alignment, nucleotide sequences are translated into protein, the alignment is performed on the protein sequence, and then translated back to nucleotide sequence. Translation alignments can be performed with any of the alignment algorithms in Geneious Prime, such as the Geneious aligner, MUSCLE or Clustal Omega.
In the translation alignment options you can set the genetic code and translation frame for the translation as well as the alignment algorithm you wish to use. Under More Options you can set the parameters such as cost matrix, gap open penalty and gap extension penalty for the alignment.