Selecting alignment regions with Seaview.

1. Load your ``OPS2'' real dataset of Rhodopsin orthologs into Seaview. The alignment is in ``fasta'' (actually multi-fasta) format, so choose ``Open Fasta.'' The data should appear at the beginning of the alignment.
   
   
2. Create a site set. When you used emma to make this alignment, what you really used was a front-end to clustalw. Notice that clustalw did not line up the N-terminal parts of all the proteins. There are a lot of gaps there. Gap-containing sites can contain useful information, but here the region is so short and the alignment looks so noisy that maybe it is better to remove this part.
   
   Now use the slider to scroll to the other end. You see that the C-terminal end of OPS2_PATYE extends out past the end of the others. You won't learn much about the evolution of these sequences by including this data! So we're going to trim both ends of the alignment by using site-sets.
   
   
   1. With your mouse click Sites -> create set. Name the region ``trimmed''. Hit OK. An extra line named ``trimmed'' with dashes (-) should appear below the alignment.
      
      
   2. Next, with your mouse, scroll back to the beginning of the alignment and click on the first (N-terminal-most) site that contains all sequences. An ``X'' should appear where you have clicked and the column above it will be highlighted with the rest of the alignment greyed out.
      
      
   3. Scroll to the other end, and find the last site (C-terminal-most) that contains all six sequences. Place the cursor there and RIGHT-CLICK to highlight all sites between the first site you clicked and this site.