Question: how to prepare an input file for Gubbins from the progressive mauve alignment output

gravatar for pradeepbe2000

3 hours ago by

I have run a progressive mauve alignment for 18 bacterial genomes. I need to prepare the input file for gubbins recombination analysis. How do i extract the core alignment and fill the gaps with n's so that i can submit the alignment file for gubbins analysis.

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