Working with data in Seaview.

Sometimes it is useful to cut an alignment up into pieces. Perhaps you want to use only part of an alignment, for instance, to analyze a certain intron or exon from a larger gene. Quite often you might want to analyze only the coding region.

Another reason to cut and trim alignments might be to throw away parts of the alignments that you don't trist, because they seem to be less informative for later work, like making trees. For instance, you might like to remove sites that contain many gaps or are poorly aligned from the final dataset that you will use for some analysis, to reduce the effects of noise that they introduce. But when you do this, be careful! The trade-off here is that you could be throwing away useful data, so you should generally trim your alignments sparingly.

At times like these you want to make a slice of your alignment. This way you take the part you need for all of your sequences at once, which saves work. Also by slicing, you let the alignment guide you about the natural boundaries of your features of interest.

One of the things that Seaview can do that Clustalx cannot is let you edit an alignment by hand. Now we'll have some practice doing sliciung and editing alignments with Seaview.