To compare large genomic DNA sequences of related organisms and of different species, researchers need efficient methods to align many long sequences. We developed a new tool Super Multiple Genome Alignment (SMGA for short), specially for rapid multiple global alignment of genomic sequences. SMGA can align a data set consisting of 50M of 9 enterobacterial genomic sequences in 40 minutes. Our method is faster when compared with other existing multiple sequences alignment method.
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