An Introduction to Phylogenetic Analysis - Association for Biology ...

64 ABLE 2005 Proceedings Vol. 27 Kosinski
Figure 6. The beginning of the ClustalW alignment of the hemoglobin beta chains of the
eight species.
This section aligns corresponding amino acids with one another so we may get an accurate estimate
of how many amino acids have changed from one species to another. A “*” under a column means
that all species had an identical amino acid in that spot, a “:” means all the amino acids were
similar, and a “.” means they were less similar, and a “ “ means one or more amino acids were
markedly different. We’re now going to use these aligned sequences to do our evolutionary
comparison.
9. Select all the text starting with “CLUSTAL W (1.82) multiple sequence alignment” and going
down to the last line of the alignment that mentions amino acid 146.
9. Use the “back” key on your browser to go back to the ClustalW page where you entered your
protein sequences. Clear all that text and paste in the contents of your clipboard. Then change the
ClustalW parameters (last line above the text box) like this:
Figure 7. Settings for the second ClustalW run. “Nj” stands for “neighbor-joining,” a technique
for doing trees. The distance and gaps setting may help to eliminate some inaccuracies.
9. Press “Run.” When your output is delivered, scroll down to the bottom and find the tree-like
cladogram. Press the button labeled, “Show as a Phylogram Tree.” To understand the phylogram
structure, refer to the phylogram below, which was done as an example using different organisms
and triosephosphate isomerase, an enzyme in glycolysis: