runRAXML: Run command line RAxML tool from within R with bootstrapping

In JosephCrispell/phyloHelpeR: Functions to help with plotting phylogenies in R

Description

Runs RAxML from within R with bootstrapping. Note that it requires raxmlHPC to available in the path.

Usage

runRAXML(
  fastaFile,
  date,
  path,
  nBootstraps = 100,
  nThreads = 6,
  outgroup = NULL,
  model = "GTRCAT"
)

Arguments

fastaFile	A character string containing the full path to the FASTA file
date	A character string corresponding to date e.g. 06-12-19 for 6th December 2019
nBootstraps	The number of bootstraps for RAxML to run. Defaults to 100.
nThreads	The number of threads for RAxML to use. Defaults to 6.
outgroup	A character string identifying a tip in the phylogeny to use as an outgroup. Defaults to NULL
model	A character string identifying the substitution model to used by RAxML

JosephCrispell/phyloHelpeR documentation built on April 7, 2020, 8:28 a.m.