Post date: Feb 06, 2014 6:37:56 PM
I decided to stick with rooted trees, although many results are similar for unrooted trees. The anna rooted trees appear particularly consistent across runs and also generate trees that are legible when plotted. So, I am going to work with these. The results for 6 or 7 admixture events are quite similar and I am going to present these as the main trees, particularly if the migration edges are significant (but perhaps include additional trees in the SI). Here is the command (-se) that I am running to (hopefully) generate jackknife se's and p-values for the migration edges with k = 6 or 7 (two replicates each because m6r2 and m7r0 were not yet ready):
/home/A01963476/bin/treemix -i /home/A01963476/projects/lycaeides_admixture/treemix/trmx_in.txt.gz -g /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_mle_rootanna__m7rep2.vertices.gz /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_mle_rootanna__m7rep2.edges.gz -se -o /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_mle_rootanna_se_m7rep2