Hello Silvia,
All of the tools in the mummer package are designed for pairwise sequence
alignment; meaning, alignment between only two genomes at a time. If by
"multiple seqs" you mean draft genomes where each genome is fragmented into
multiple contigs, simply pass nucmer two multi-fasta files containing all
the sequences (one file for each genome). However, if you want to align
multiple whole genomes, you will need a multiple alignment program. You
could try MGA:
http://bibiserv.techfak.uni-bielefeld.de/mga/
or Multi-lagan:
http://lagan.stanford.edu/lagan_web/index.shtml
Good luck,
-Adam
On Tue, Mar 3, 2009 at 1:56 PM, Silvia E. Smith <sil...@gm...>wrote:
> Hi All,
> I am new to MUMmer and I need to align multiple whole bacterial
> genomes. I was able to align two whole genomes in NUCMER (one as the ref
> and the other as the query) with this command:
>
> /nucmer --maxgap=50000 --mincluster=1 --prefix=ref_qry ref.fasta qry.fasta
>
> /show-coords -r -c -l nucmer.delta > nucmer.coords
> /show-aligns ref_qry.delta "jay" "bob" > ref_qry.aligns
>
> How do I align multiple seqs?
>
> Thanks!
>
> Silvia
>
>
>
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