Treemix

Treemix

01. build the ML tree

treemix -i treemix.input.gz -k 1 -o 02.ML.tree -root AF-YRI,AF-LWK,AF-GWD,AF-MSL,AF-ESN,AF-ASW,AF-ACB

02. build the ML graph with migration

treemix -i treemix.input.gz -k 1 -m 1 -root AF-YRI,AF-LWK,AF-GWD,AF-MSL,AF-ESN,AF-ASW,AF-ACB -o 03.treemix.1
treemix -i treemix.input.gz -k 1 -m 2 -root AF-YRI,AF-LWK,AF-GWD,AF-MSL,AF-ESN,AF-ASW,AF-ACB -o 03.treemix.2
...
treemix -i treemix.input.gz -k 1 -m 10 -root AF-YRI,AF-LWK,AF-GWD,AF-MSL,AF-ESN,AF-ASW,AF-ACB -o 03.treemix.10

03. plot

source("treemix/treemix-1.12/src/plotting_funcs.R")

# tree
pdf(paste(stem,"tree.pdf",sep="."))
plot_tree(stem,"poporder")
dev.off()

# residual visualization
pdf(paste(stem,"residual.pdf",sep="."))
plot_resid(stem, "poporder")
dev.off()