Generate bash commands to generate phylogenies with RAxML

Source: R/phyloscan.fun.scripting.R

This function generates bash commands to generate one phylogeny with RAxML, that can be called via 'system' in R, or written to file to run on a UNIX system.

raxml.cmd(infile.fasta, outfile = paste(infile.fasta, ".newick", sep = ""),
  pr = "raxmlHPC-SSE3", pr.args = "-m GTRCAT --HKY85 -p 42")

Arguments

infile.fasta

Full path name to input fasta file.
outfile

Full path name to output file. All RAxML output other than the best tree will be zipped and returned as 'outfile.zip'.
pr

Full path name to RAXML program.
pr.args

RAXML arguments.

Value

Character string