Massive Scaling of Alignments

Within this decade it will become common to have dozens or even hundreds of completed genomes for viruses. Current tools are not capable even of aligning all the HIV genomes in Genbank. (The extreme divergence, recombination, and lack of DNA repair mechanisms in HIV make it impossible for an anchor-based multiple alignment technique like MGA to locate common anchors, and nonanchor alignment techniques like DIALIGN fail on the more than 300 HIV genomes now available.) Space and time constraints need to be constantly pushed back as the cost of acquiring genomic sequence continues to plummet.

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