raxml.cmd: Generate bash commands to generate phylogenies with RAxML

In olli0601/phyloscan:

Generate bash commands to generate phylogenies with RAxML

Description

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.

Usage

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

olli0601/phyloscan documentation built on April 25, 2024, 4:16 a.m.