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  • Aligning multiple small viral genomes

    Hi all,
    For a sequencing project I need to align multiple (>100) small (<6kb) viral genomes. Which is the best algorithm to use? I tried Mauve and it seems to work fine, but the results are indeed confusing, with so many sequences.
    What would you suggest?

    -MikeT

  • #2
    Are these genomes homologous/mostly identical? You should perhaps try more conventional MSA programs like clustal, t-coffee or muscle in that case.

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