I am working with bacterial whole genome sequences. I understand I have to do a multiple alignment (for which I used parsnp on my de novo assembled genomes) and remove recombination first. I detected the recombination sites with Gubbins but did not get an output of multiple alignment where the recombination sites are removed. So now I am unsure as to how to proceed. I assume I have to somehow remove this recombination sites and convert the alignment to a nexus file for BEAUTi. Alternative ways to proceed are also appreciated. Thanks in advance!
Question: How to prep an input (nexus) file for BEAST/BEAUTi?
14 months ago by
hallishtw • 10
hallishtw • 10 wrote:
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