Run the entire phylotaR pipeline. All generated files will be stored in the wd. The process can be stopped at anytime and restarted with restart. nstages must be a numeric value representing the number of stages that will be run. Stages are run in the following order: 1 - taxise, 2 - download, 3 - cluster and 4 - cluster2.

For example, specifying nstages = 3, will run taxise, download and cluster. Stages can also be run individually, see linked functions below.

run(wd, nstages = 4)



Working directory


Number of total stages to run, max 4.

See also



  # Note: this example requires BLAST and internet to run.

  # example with temp folder
  wd <- file.path(tempdir(), 'aotus')
  # setup for aotus, make sure aotus/ folder already exists
  if (!dir.exists(wd)) {
  ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
  # e.g. "/usr/local/ncbi/blast/bin/"
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  run(wd = wd)
# }