Retrieve sequences from genbank — sq.retrieve.direct • phruta

Downloads sequences from genbank (nucleotide database) for particular taxa and genes into a folder called "0.Sequences".

Usage

sq.retrieve.direct(
  clades = NULL,
  species = NULL,
  genes = NULL,
  db = "itis",
  maxseqs = 1,
  maxlength = 5000
)

clades: A vector listing taxonomic groups of interest (character).
species: A vector listing additional species interest (character). This argument can be used to define additional target species in the ingroup or species to be sampled in the outgroup (character).
genes: A vector listing gene names of interest (character).
db: Follows db in taxize::downsteam. Choose from itis, gbif, ncbi, worms, or bold.
maxseqs: Maximum number of sequences to retrieve per search (taxa + gene) (numeric).
maxlength: Maximum length of the gene sequence (numeric).

None

if (FALSE) {
sq.retrieve.direct(
  clades = c("Felis", "Vulpes", "Phoca"),
  species = "Manis_pentadactyla",
  genes = c("ADORA3", "CYTB")
)
}