execSeqGen: Execute seq-gen

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

Description

Generate sequences with seq-gen using parameters from the RAxML run

Usage

execSeqGen(params, nreps, model = "GTR", ngamma = 4, seed = "10101",
  outputFormat = c("relaxed", "phylip", "nexus"),
  pathSimData = "simDataGrouped")

Arguments

params	The list of parameters generates by getParams
nreps	Number of replicated alignments to generate
model	Model of molecular evolution used to generate the data (for now only ‘GTR’ is supported)
ngamma	Number of categories for the alpha parameter of the Gamma distribution (RAxML always uses 4, so you should probably leave it as the default value of 4).
seed	Seed number to generate the alignment
outputFormat	Format file of the alignment generated by seq-gen, if you intend to use RAxML to estimate your trees, keep the default (‘relaxed)’.
pathSimData	Where the output files will be stored (default ‘simDataGrouped’)

Details

Currently, seq-gen uses a proportion of invariant sites depending on whether the list of parameters in the params object is empty or not.

Value

TRUE, but really is used for its side effect of generating random sequences stored in files.

Author(s)

Francois Michonneau

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