library(ape)
library(ips)
myalignment <- read.dna("ray2000_aligned.fas",format="fasta",as.matrix=TRUE)
The raxml
function is just a wrapper around the external program, and so this will need to be installed separately.
myalignment.rax.gtr <- raxml(myalignment,
m="GTRGAMMAIX", # model
f="a", # best tree and bootstrap
p=1234, # random number seed
x=2345, # random seed for rapid bootstrapping
N=100, # number of bootstrap replicates
file="ray2000", # name of output files
exec="raxmlHPC-PTHREADS-SSE3", # name of executable
threads=2
)