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Old 03-13-2015, 12:30 AM   #1
MikeT
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Default 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
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Old 03-13-2015, 02:58 AM   #2
GenoMax
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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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