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parsnp and out-groups

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

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updated 4.7 years ago by ahmed_elsherbini91 •

• written 5.9 years ago by jellila •

1 answer

did you find a solution for this issue

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written 4.7 years ago by ahmed_elsherbini91 •

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