Re: [MUMmer-help] 1-to-1 and m-to-m

[Adam P. <aph...@gm...>]

A very rough explanation: All the alignment intervals on the reference and
query are scored based on some combination of their length and identity,
and a subset are marked as the "best" alignment for that region of the
genome. -m keeps any alignment that is marked best on EITHER the reference
OR query. -1 keeps only alignments that are marked best on BOTH the
reference AND query. Another way of saying it: if there is a duplication in
the query genome, -m will attempt to keep alignments from the ancestral
copy in the reference to both paralogs in query. -1 will only keep the
alignments between orthologs, and the duplication will remain unaligned.
Both options are heuristics and don't always work perfectly, but can be
helpful in reducing the number of repetitive alignments in the output.

Best,
-Adam


On Sun, Oct 7, 2018 at 5:11 AM Arun Prasanna <aru...@gm...>
wrote:

> Hello,
>
> Can anyone please tell me the meaning of M-to-M alignments mean ? I
> understood that 1-to-1 means number of unique alignments.
>
> Thanks,
> AP
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