MGA (Multiple Genome Aligner) computes multiple genome alignments of large, closely related DNA sequences. MGA is a software tool for efficiently aligning two or more sufficiently similar genomic sized sequences [HKO02]. It belongs to the category of anchor-based multiple alignment methods. mga uses multiMEMs (or MEMs, MUMs as special cases) to anchor the alignment. In essence, they are (hopefully long) stretches or regions of identical bases occuring in all input sequences.
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Michael Höhl, Stefan Kurtz, Enno Ohlebusch
Efficient Multiple Genome Alignment
Bioinformatics, Vol. 18 (S1): S312-S320, 2002.