Treemix

[Eddy Dowle]

HI
Im trying to run Treemix on a non-model species with some RAD data.
Im just wondered if treemix can deal with missing data on some populations or do the SNPs need to occur across all the populations? Currently Im just collapsing all my individuals from a population into one string for each population (Im assuming that is right). I just wondered what the 0 in SNP input file in the manual meant, I was assuming that was missing data but they also occur next to a called SNP (1,2,3,4)
pop1 pop2 pop3 pop4
5,1 1,1 4,0 0,4

Thanks
Eddy

[Joseph Pickrell]

Hi Eddy,

The two numbers in the input file are the counts of the two alleles.
Completely missing data would be 0,0 (for 0 counts of the first allele
and 0 counts of the second allele). The entry 0,4 means that there are
4 observed alleles and all of them are of the second type.

Cheers,

Joe

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