A new approach to multiple sequence alignment is proposed. One takes a set of sequences to align, modify a guide phylogenetic tree to obtain a Steiner tree (which we refer to in this context as a Spannoid), align the full components of the tree and combine them into one alignment using the internal sequence nodes as a scaffold. The method is flexible, with the optimality and speed of alignment dependent on the size of the components and the component alignment method. This provides a fast method of aligning thousands of sequences. We give data on the detrimental effect on the final alignment that dividing the problem up in this manner does to assess the reliability alignments of thi
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