megapteraProj: Bundle Input Data for the Pipeline
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Value References See Also

Create an object of class megapteraProj to hold all the input data necessary for running of the pipeline.

megapteraProj(
  db,
  taxon = taxon(),
  locus = locus(),
  align.exe = "undefined",
  merge.exe = "undefined",
  mask.exe = "undefined",
  params = megapteraPars(),
  update = FALSE
)

`db`	An object of class `dbPars`.
`taxon`	An object of classes `taxon` or `taxonGuidetree`.
`locus`	An object of classes `locus` or `locusRef`.
`align.exe`	A vector of mode `"character"`, giving name of the alignment program; currently only MAFFT is allowed.
`merge.exe`	A vector of mode `"character"`, giving name of the alignment merging program; currently only OPAL is allowed.
`mask.exe`	A vector of mode `"character"`, giving name of the alignment masking program; currently only Gblocks is allowed.
`params`	An object of class `megapteraPars`.
`update`	Logical: if `TRUE`, the pipeline's steps are executed as if called for the first time, i.e., possibly overriding data and setting that have been previously achieved.

An object of class megapteraProj.

MAFFT: http://mafft.cbrc.jp/alignment/software/

OPAL: http://opal.cs.arizona.edu/

Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html

dbPars, taxon, taxonGuidetree, locus, locusRef, and megapteraPars for defining of database parameters, taxa, loci, and the pipeline's parameters, respectively.