Hello,
after reading some of the closed comments I thought that I make my question more specific: is there any reason to include an outgroup with the -C option? If I include an outgroup, I am loosing SNPs (as the outgroup has more missing data, so I am wondering if it is better to use less SNPs but specify the outgroup or use more SNPs and don't specify the outgroup.
Thank you!
Hello,
after reading some of the closed comments I thought that I make my question more specific: is there any reason to include an outgroup with the -C option? If I include an outgroup, I am loosing SNPs (as the outgroup has more missing data, so I am wondering if it is better to use less SNPs but specify the outgroup or use more SNPs and don't specify the outgroup.
Thank you!