Alignment Of Consensus Sequences

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An example consensus alignment view.

An extremely useful tool in checking and correcting assembly results is an alignment of consensus sequences. This can also be done using Geneious. To create an alignment of consensus sequences select all of the contigs you want to use and click Alignment in the toolbar.

Under Consensus Align select "Create alignment of consensus sequences only" and choose your favored alignment algorithm, eg. ClustalW. Click OK and an alignment will be created and selected:

The alignment retains references back to the contigs that it was built from so you can click on the small blue arrow button to the left of each name to jump to the associated contig. Geneious currently doesn't propagate changes in the alignment back to the contig but you can use the alignment for downstream steps so any edits are not lost.


Firstly, to set up viewing of the alignment using the translation follow these steps:

  1. In the options to the right of the alignment view change the Colors option to "By Translation"
  2. Turn off the Highlighting option
  3. Open the Complement & Translation section and set up the appropriate translation options such as genetic code and frame. You can also set the amino acid color scheme here (eg. MacClade).
  4. You should also turn off Annotations so that editing history annotations don't interfere with the layout.


Now you can scan through the alignment looking for frame shifts and stop codons, correcting as necessary.

It is recommended you click on Help in the toolbar while viewing an alignment and read the brief documentation there on editing and shortcut keys.