Skip to Content
Auckland campus is closed at COVID-19 Alert Level 3. More information.
What is a Quagga?
Making a Sequence Alignment
A sequence alignment is a way of organising related sequences so that the differences among them show evolutionary change.
Here you will import the sequences obtained by the Wilson group into a desktop program called Geneious to complete the alignment and subsequent phylogenetic analysis. Geneious is a popular program for managing and analyzing DNA sequences.
Take a few minutes now to download and install Geneious, and become familiar with navigating in the program. Return to this window when you are ready to proceed with the Quagga story. [Get Geneious]
Get the sequences
If you have already downloaded the sequence file, then skip ahead.
You will need the file of DNA sequences obtained the Wilson group. Whatisaquagga (1 KB) Right-click on the sequence image, choose Save the Link As ... and save the file on your desktop computer.(Please extract zip file before use) .
Import the Quagga Sequences
The sequences obtained by the Wilson group need to be imported into Geneious.
Make a working folder to store your analysis.
Import the sequences.
The sequences will now be listed. You can view them individually by clicking on each in turn.
As you scan through them, notice that the sequences for the nd1 and co1 regions are inter-mixed.
Align the sequences
You need to construct two sequence alignments, one for each of nd1 and co1.
Return to the Research Plan for the next step.