Clustal (1) has been part of the Sequencher family of plugins since version 4.9. It is a widely used multiple sequence alignment program which works by determining all pairwise alignments on a set of sequences, then constructs a dendrogram grouping the sequences by approximate similarity and then finally performs the alignment using the dendogram as a guide. You can use Clustal to align your sequences directly from the Sequencher project window. Choose from a range of parameters to control the alignment process.
Once the alignment is complete you will see the results as a contig or contigs within Sequencher which you can subject to a variety of analyses.
Speed up your Clustal alignments by combining Clustal with the power of Sequencher's Assemble by Name functionality for aligning multiple sequences from different sources.
Finally, export the results in a variety of different formats such as MSF, Phylip, NEXUS and FastA for use in other programs or simply create a consensus and export it.
1. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003). "Multiple sequence alignment with the Clustal series of programs". Nucleic Acids Res 31 (13): 3497-3500