generateAlignments: Generate Simulated alignements
In fmichonneau/rsowh: rsowh - an R interface for the SO-WH test

Description Usage Arguments Details Value Author(s)

This function takes an alignment (with partition information if needed), a tree, and simulate datasets under a given model according to the guide tree provided. Each partition is optimized on the guide tree for all the model parameters (transition rates, base frequencies, gamma parameter, and proportion of invariants).

generateAlignments(algfile, partfile, tree, model, nreps,
  formatin = "sequential", pathFiles = ".",
  pathResults = file.path(pathFiles, "simDataGrouped"),
  raxmlCmd = "raxmlHPC-PTHREADS-SSE3", raxmlArg = "-T7")

`algfile`	The original alignment file, can be in any format supported by ape:::read.dna
`partfile`	The partition file (at this stage only RAxML partition files are supported)
`tree`	A tree file in Newick format
`model`	The model of molecular evolution to be used for parameter estimation on each parameters (at this stage, only “`GTRGAMMA`” and “`GTRGAMMAI`” are supported).
`nreps`	Number of replicated simulated datasets to generate.
`formatin`	The alignment format needs to be a format supported by ape::read.dna.
`pathFiles`	Character string indicating the path where the data files (`algfile`, `partfile`, `tree`) as well as `seq-gen` are located. Default if current working directory.
`pathResults`	Character string indicating the path where the files generated by this function will be written. Default is a subdirectory of `pathFiles` named `simDataGrouped`.
`raxmlCmd`	Which RAxML flavor do you want to use? (default raxmlHPC-PTHREADS-SSE).
`raxmlArg`	Additional arguments to be passed to RAxML.