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Choice of outgroup #2
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Hello! The outgroup is used in NCD2 (but not NCD2). NCD2 outperforms NCD1, so is preferable. The way this information is used is as follows:
I hope this helps! |
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Dear Bárbara,
Thank you for developing this method and useful software.
I want to ask some questions about the choice of the outgroup. I want to use NCD2 to detect the signature of balancing selection in the genome of a fish species. There is a sister species that has a divergent time of 2 MYA to my fish species, and this species also have a similar trait that is hypothesized under balancing selection. However, I will only focus on my species, since there are not enough samples of its sister species. Do you think is it appropriate to use its sister species as an outgroup? Does the divergent time (2 MYA) matter? And a more important question, should I choose another species without the candidate trait of interest as an outgroup, or it doesn't matter since even though the same gene contributes to this trait in two species, the substitutions should be different since the surrounding loci are caused by mutations.
Thanks in advance!
Best wishes,
Xiaomeng
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