Run the third stage of the phylotaR pipeline, cluster. This stage hierarchically traverses the taxonomy identifying all direct and subtree clusters from downloaded sequences. Any taxonomic nodes too small for cluster identification are placed into paraphyletic clusters.
See also
Other run-public:
ClstrArc-class,
ClstrRec-class,
Phylota-class,
SeqArc-class,
SeqRec-class,
TaxDict-class,
TaxRec-class,
clusters2_run(),
parameters_reset(),
reset(),
restart(),
run(),
setup(),
taxise_run()
Examples
if (FALSE) { # \dontrun{
# 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]'
setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr) # txid for Aotus primate genus
# individually run stages
taxise_run(wd = wd)
download_run(wd = wd)
clusters_run(wd = wd)
} # }