Aligning multiple small viral genomes

[MikeT]

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

[GenoMax]

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