Question: parsnp and out-groups
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gravatar for jellila
6 months ago by
jellila0
jellila0 wrote:

Hi,

I am trying to build some phylogenetic trees based on core genome SNPs in bacteria using parsnp. However, I have a doubt. If I include only my strains in the alignment then my tree will be unrooted. If I want a rooted tree then I will have to include an out-group. However, if I include the out-group then my core genome is not accurate anymore, as I will be cutting it down considerably. Any thoughts about this matter? I am really confused!

Thanks.

Laura

parsnp phylogeny • 192 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 6 months ago by jellila0
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