Rscript_collapse_polytomies.txt

# Rscript_collapse_polytomies.txt

# usage:
# Rscript Rscript_collapse_polytomies.txt intrees_file outtrees_file

library(geiger)

args = commandArgs(trailingOnly=TRUE)
fileName = args[1] ## "RADtag_trees_phylogeny_major_groups.txt"
outfilename = args[2] ##"RADtag_trees_phylogeny_major_groups.collapsed_polytomies.txt"

conn <- file(fileName,open="r")
linn <-readLines(conn)
for (i in 1:length(linn)){
	print(i)
	intree <- read.tree(text = linn[i])
	collapsed_polytomies <- di2multi(intree, 0.00001)

	write.tree(collapsed_polytomies, file = outfilename, append = TRUE,
           digits = 10, tree.names = FALSE)

}
close(conn)