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


if (FALSE) { # 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)) { dir.create(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) }