bootstraped treemix show no migration event
Entering edit mode
11 weeks ago
reza ▴ 300

I run treemix with bootstraping using (BITE R package) with one migration event. it worked without any error. Now when I want to draw the tree, the tree is drawn but without any migration event and I get the following warning message.

Warning message:
In max(e[e[, 5] == "MIG", 4]) :
  no non-missing arguments to max; returning -Inf

I have used the following commands for this analysis:

./ treemix.gz 1 8 1000 horse 100 ~/phylip-3.697/exe/consense out_bootstraped




treemix.bootstrap(in.file = "infile_bootstraped",
                  out.file = "test",
                  phylip.file = "bootstraped_outtree.newick", nboot = 100,
                  cex=0.5, xmin = -0.005, disp = 0.001,
                  boot.legend.location = "top", xbar = 0.05)

Updated: For more clarify

The interesting thing is that after running the program for each number of migration event (m), in the tree visualization stage, the number of observed migration events on constructed tree is one less than the number of migration event in the previous stage. For example, I run program based on two migration events, but its visualized tree shows only one migration event, and when I run it with one event, its tree does not have any migration event. Please, those who have worked in this field, help me to solve this issue

Treemix Bootstrap • 236 views

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