cmd.examl.bootstrap: Generate the ExaML boostrap shell command, one bootstrap per...

In olli0601/big.phylo: big.phylo

Description

Internal code.

Usage

cmd.examl.bootstrap(indir, infile, bs.from = 0, bs.to = 99,
  bs.n = bs.to - bs.from + ifelse(bs.from == 0, 1, 0), outdir = indir,
  prog.mpi = "mpiexec", prog.bscreate = PR.EXAML.BSCREATE,
  prog.parser = PR.EXAML.PARSER, prog.starttree = PR.EXAML.STARTTREE,
  prog.examl = PR.EXAML.EXAML, opt.bootstrap.by = "codon",
  args.examl = "-m GAMMA -D", args.parser = "-m DNA",
  prog.supportadder = PR.EXAML.BS, tmpdir.prefix = "examl",
  resume = 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
bs.from	Iteration number of bootstrap calculations. Defaults to 0.
bs.to	Final iteration number of this call to pipeline.ExaML.bootstrap.per.proc. Defaults to bs.n.
bs.n	Total number of boostrap iterations. Defaults to 500.
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.