Post date: Feb 04, 2014 10:15:18 PM
Some of the treemix analyses from yesterday are done but some are still running. Two things are apparent (i) the basic tree toplogy is not always the same, and (ii) my specified roots wre not always possible. So, I decided to first calculate a ML tree, use that tree to specify a valid root that includes L. anna (the first major split), and then add migration events to the rooted tree. Here are the exact steps commands I used:
Infer ML tree
treemix -i trmx_in.txt.gz -o trmxout_mle
Root tree with anna/ricei clade
treemix -i trmx_in.txt.gz -o trmxout_mle_rootanri -g trmxout_mle.vertices.gz trmxout_mle.edges.gz -root BIG,MBM,SHC,SMR,MTR,DOP,YBG,CPE,LKS,FCR
Infer migration edges
/home/A01963476/bin/treemix -i /home/A01963476/projects/lycaeides_admixture/treemix/trmx_in.txt.gz -m 10 -seed 362 -g trmxout_mle_rootanri.vertices.gz trmxout_mle_rootanri.edges.gz -o /home/A01963476/projects/lycaeides_admixture/treemix/results/trmxout_rootanri_m10rep2
Migration analysis with 1 to 10 migration events are running on the dorc.