bbitarello / ncd-statistics Goto Github PK

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

Hello，
If I use balselr's parse_vcf.R to get the input file for NCD2, how do I calculate NCD2 in NCD-statistics? Because I didn't know how to compute NCD2 in balselr

Thanks

Hi,

I have calculated the NCD1 values using the function NCD1(). I want to ask how to calculate the P values for such NCD1 values?

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