Consensus Alignment allows you to align two or more alignments together (and create a single alignment) and align a new sequence in to an existing alignment. Select the sequences or alignment you wish to align and select the Align/Assemble button from the Toolbar and choose Multiple Alignment. Consensus alignment allows you to choose which alignment algorithm to use for aligning the consensus sequences. All of the pairwise and multiple alignment algorithms are available. The consensus sequence used for each alignment is a 100% consensus with gaps ignored.