Run the fourth stage of the phylotaR pipeline, cluster2. Identify clusters at higher taxonomic levels by merging sister clusters.
See also
Other run-public:
ClstrArc-class,
ClstrRec-class,
Phylota-class,
SeqArc-class,
SeqRec-class,
TaxDict-class,
TaxRec-class,
clusters_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)
clusters2_run(wd = wd)
} # }