Post date: Feb 05, 2014 11:39:40 PM
I am still not sure what to think about rooting the tree. I would rather not if I can get consistent answers without doing this. I am running treemix based on the unrooted ML tree for k= 1 to 10 with 3 reps.
/home/A01963476/bin/treemix -i /home/A01963476/projects/lycaeides_admixture/treemix/trmx_in.txt.gz -m 10 -seed 162 -g /home/A01963476/projects/lycaeides_admixture/treemix/trmxout_mle.vertices.gz /home/A01963476/projects/lycaeides_admixture/treemix/trmxout_mle.edges.gz -o /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_mle_m10rep2
I decided run yet another iteration, but with anna (L. anna anna = FCR, DOP, YBG, LKS, CPE) as the root. The files are *rootanna*.