A rough and ready test of ips::raxml()

Testing_ips_raxml.R

# testing ips
library(ips)
library(phyloseq)

# load in example data
data(ips.cox1)
data(ips.16S)
data(ips.28S)

ips <- cbind(ips.cox1, ips.16S, ips.28S,
fill.with.gaps = TRUE)

# set path for RAXML is
# CHANGE THIS
exec <- '~/Desktop/standard-RAxML-master/raxmlHPC-SSE3'

# setwd - CHANGE THIS
setwd('~/Desktop')

# run raxml
tr <- raxml(ips,
m = "GTRGAMMAIX", # model
f = "a", # best tree and bootstrap
p = 1234, # random number seed
x = 2345, # random seed for rapid bootstrapping
N = 5, # number of bootstrap replicates
exec = exec, # name of executable
file = 'raxml_example',
threads = 20
)

tree <- read_tree("RAxML_bipartitionsBranchLabels.raxml_example")