RCmds

# two R dependencies (packages) are required, ips and parallel
# While in R, use install.packages(c("ips", "parallel")) to install.

library(ips)
library(parallel)
setwd("/my/working/directory/")
files=list.files(pattern = '.nexus')
nex = length(files)
# get number of files for 1:length(1:n files)

for(i in 1:length(1:nex)){
       phylip = read.nex(files[i])
       this.name = files[i]
       newname=sub(".nexus",".phy",files[i])
       print(newname)
       save.path = getwd()
       save.path = paste(save.path,"/",sub(".nexus","",files[i]),sep = "")
       write.phy(phylip, file=file.path(save.path, newname), interleave=FALSE)
}
phy_files_list = list.files(pattern = "*.phy$", recursive = TRUE, path = getwd(), full.names = TRUE)

cmd =list()

for(i in 1:length(phy_files_list)){
       cmd[[i]] = paste(getwd(), "/run_RAxML.sh ", phy_files_list[i], sep="")
}
# make sure your  system has 48 cores or change the 48 to an appropriate number of threads.
final_raxml = mclapply(cmd, system, mc.cores=getOption("mc.cores", 48))  ### 48 threads