cmd.examl.single: Produce a single ExaML shell command.

In olli0601/big.phylo: big.phylo

Description

Internal code.

Usage

cmd.examl.single(indir, infile, outdir = indir, outfile = infile,
  prog.mpi = "mpiexec", prog.bscreate = PR.EXAML.BSCREATE,
  opt.bootstrap.by = "nucleotide", prog.parser = PR.EXAML.PARSER,
  args.parser = "-m DNA", prog.starttree = PR.EXAML.STARTTREE,
  prog.rndstarttree = PR.EXAML.BS, args.starttree.seed = 12345,
  args.starttree.type = "parsimony", prog.examl = PR.EXAML.EXAML,
  args.examl = "-m GAMMA -D", bs.seed = floor(runif(1, 10000, 1e+05 -
  1)), verbose = 1)

Arguments

indir	Directory of the sequences in file infile
infile	File name to an DNAbin matrix. The file name must end in .R
outdir	Output directory for the bootstrap calculations
verbose	Flag to run function in verbose mode.

Value

Character string

olli0601/big.phylo documentation built on Nov. 9, 2019, 9:25 a.m.