Multiple Sequence Alignment - Build the alignment

You will now use Geneious Prime to align the plant DNA sequences provided plus the new sequence you found in the BLAST search section.

The tutorial folder contains a set of 22 DNA sequences which can be identified by the nucleotide () icon. In addition, the sequence from your BLAST search will also be a DNA sequence with the same icon. Select all of the DNA sequences in the tutorial folder. Make sure you do not select the tutorial document itself because if you do, the alignment button will not work.

With all 23 sequences selected, click on Align/Assemble→Multiple Align (or in the Tools menu if you prefer). We will perform an alignment using MUSCLE as it is faster than the Geneious aligner, so select this option. Keep all the other settings at their defaults.



Click the OK button. After the alignment is completed, the alignment document, (), will appear in the Document Viewer panel and the document should open automatically.

Inspect the alignment in the Alignment View tab.


Question 4: Where have most of the gaps been placed?
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View the annotations of the sequence you imported from the BLAST search in the alignment. If you cannot see the annotations you need to turn on annotations in the Annotations and Tracks panel to the left of the alignment viewer.


Question 5: Which domains show the most variability and the least variability among all of the sequences?
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Expand the Statistics panel on the right side of the Alignment View tab.

Question 6: What is the pairwise % similarity of the sequences and the percentage of sites that are identical?
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Question 7: Why do these two numbers differ?
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Exercise 3: Molecular Phylogenetics