With the MSA views dialog, you can specify how you want the alignment results displayed. You can choose from the following output options:
- multiple alignment text display
- pairwise alignment text display
- multiple alignment picture display
- guide tree
- consensus sequence display.
- Matrix
- Profile
Each results page is displayed as a separate tab in the The MSA Editor. If a tab is greyed out that results page has not yet been calculated. Note Muscle does not generate a Guide Tree.
The Profile tab displays the frequency of occurrence of each residue at each position in the alignment. Although primarily designed to simply display the information along with the consensus sequence, the text is in Transfac format, so you can save this information (using File | Export) and use it in other applications (including the NA Analysis Toolbox in the case of DNA sequences).
If you want to recalculate the alignment, select ALIGN.
Displaying shared domains across protein alignments.
Performing a ClustalW alignment