How do I align entire sequences or subsequence regions?
To align sequences in BBB, first select the sequences you wish to align (by clicking on their names in the Sequence List.) Choose the “Select” mouse mode from the toolbar and select the sequence region that you wish to align. Selecting large regions can be done more easily by using the “Select Region” tool from the Edit menu. To select the entire sequence, choose the “Select Whole Sequence” option from the Edit menu.
Finally, go to “Align Selection” under the “Tools” menu; choose the method of alignment (ClustalW, TCoffee, or Muscle (proteins only)) you wish to use. Adjust the alignment parameters (if necessary) and wait for the alignment to be generated (this may take several minutes or longer for large sequences.) When the results window appears, click “Ok” to accept the alignment.