sq.retrieve.direct: Retrieve sequences from genbank

In cromanpa94/phruta: Phylogenetic Reconstruction and Time-dating

Retrieve sequences from genbank

Description

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

## Not run: 
sq.retrieve.direct(
  clades = c("Felis", "Vulpes", "Phoca"),
  species = "Manis_pentadactyla",
  genes = c("ADORA3", "CYTB")
)

## End(Not run)

cromanpa94/phruta documentation built on May 7, 2023, 4:09 a.m.