Consensus sequence maker which gives per base % on the command line?

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8.1 years ago

mdrnao • 0

Hi all,

I am trying to find a consensus sequence maker that can take a nucleotide MSA but the most important part is I need it provide per base percentages.

I can use Jalview desktop app for this, but as I have ~80 alignments I was hoping to find a command line program that has this functionality so I can loop through files? The command line programs I have found only provide the sequence??

Thanks

MSA alignment • 2.0k views

ADD COMMENT • link 8.1 years ago by mdrnao • 0

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Jalview can be run on the command line (http://www.jalview.org/help/html/features/clarguments.html ). Perhaps that will work.

ADD REPLY • link 8.1 years ago by GenoMax 149k

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Yes, I have seen this. But either I'm incapable or its incapable to be able to create the consensus and the %id! Sadly, I can't figure out which :)

ADD REPLY • link 8.1 years ago by mdrnao • 0

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You could email them via the Jalview-discuss list and see if that gets you additional info.

ADD REPLY • link 8.1 years ago by GenoMax 149k

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