Convert RAxML consensus tree | Readable in R | APE library

parse_raxml_newick.R

# LIB
library(ape)

# DATA
# tree string produced by `RAxML -J ` arg
trstr <- "(A,B,(C,((D,((E,F):1.0[80],((G,H):1.0[100],(I,J):1.0[100]):1.0[67]):1.0[58]):1.0[98],(K,(L,(M,N):1.0[89]):1.0[91]):1.0[100]):1.0[97]):1.0[97]);"

# FAIL
tree <- read.tree(text=trstr)
# node.label = NULL

# CONVERT STRING
# remove branch lengths and []
trstr <- gsub(':[0-9.]+', '', trstr)
trstr <- gsub('(\\[|\\])', '', trstr)

# SUCCESS
tree <- read.tree(text=trstr)
# node.label = ""    "97"  "97"  "98"  "58"  "80"  "67"  "100" "100" "100" "91"  "89"
# Note, branch lengths are lost