generateRAxMLscripts: Generate RAxML scripts

In fmichonneau/rsowh: rsowh - an R interface for the SO-WH test

Description

Wrapper for all the functions up to the point of running the RAxML analyses. Really the only function you should be using.

Usage

generateRAxMLscripts(path, model, algfile, partfile, treefile, nreps,
  constrTopology, prefixConst = "const", prefixBest = "best", seed)

Arguments

path	root path (i.e., directory) within which all the file manipulations will be performed.
model	The model of molecular evolution to be used in the analysis (only GTRGAMMA and GTRGAMMAI supported for now)
algfile	Path to the original alignment file
partfile	Path to the original partition file
treefile	Path to the CONSTRAINED (H0) tree
nreps	Number of replicated datasets to use in the simulations
constrTopology	Path to the CONSTRAINED multifurc*ating topology
prefixConst	Character string indicating the prefix for the files generated for the constrained topology
prefixBest	Character string indicating the prefix for the files generated for the unconstrained topology
seed	The seed to be used for the analyses (same seed is used by seq-gen and RAxML)

Details

This function generates bash scripts that contain the appropriate calls to RAxML to estimate the likelihoods based on constrained and unconstrained searches.

The ‘path’ should contain all the files used to initiate the data set simulation and analyses.

Value

TRUE, but used for its main effect of generating the bash scripts needed to run the SOWH test.

Author(s)

Francois Michonneau

fmichonneau/rsowh documentation built on May 16, 2019, 1:47 p.m.