Post date: Feb 03, 2014 8:17:56 PM
I am using treemix to infer the location of admixture events on a population tree of the Lycaeides populations (localities). I am running the analysis with 1 to 15 admixture events (I need to run 0 admixture events too). For each k (# of events) I am setting (a) no root, (b) a root with anna, and (c) a root with the western melissa populations, and I am running each analysis three times with different seeds. Here is an example with the three different roots:
/home/A01963476/bin/treemix -i /home/A01963476/projects/lycaeides_admixture/treemix/trmx_in.txt.gz -m 13 -seed 177 -o /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_noroot_m13rep0
/home/A01963476/bin/treemix -i /home/A01963476/projects/lycaeides_admixture/treemix/trmx_in.txt.gz -m 13 -root DOP,FCR,LKS,YBG,CPE -seed 177 -o /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_annaroot_m13rep0
/home/A01963476/bin/treemix -i /home/A01963476/projects/lycaeides_admixture/treemix/trmx_in.txt.gz -m 13 -root BHP,GVL,REW,SLA,VCP,WAL -seed 177 -o /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_melwroot_m13rep0
The analysis is running on the dorc with treemix 1.12 and the results are being written to projects/lycaeides_admixture/treemix/results/. I am not yet sure whether the p-values for each admixture event are automatically calculated and included in the output.