Hi Rajeh, I suggest you read the algorithm description in this paper:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011147
which discusses this issue.
On Tue, 2015-11-17 at 17:09 -0600, Ahmad Rajeh wrote:
> Hello,
>
> I have a question about Mauve’s algorithm: How does Mauve deal with contigs
> that are found in more than one region in the reference? I tried to test this
> by aligning a contig I had to a reference containing the same contig twice.
> Mauve only aligned the contig to the first occurrence in the reference. Is
> that how mauve deals with multiple alignments–by picking the first alignment?
>
> Thanks,
> Rajeh
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