RAxML exercise

Load the libraries

library(ape)
library(ips)

Read in the data

myalignment <- read.dna("ray2000_aligned.fas",format="fasta",as.matrix=TRUE)

Run RAxML

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
      )