Skip to contents

Retrieve sequences from genbank

Source: R/sq.retrieve.direct.R
sq.retrieve.direct.Rd

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
)

Arguments

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).

Value

None

Examples

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