Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names.
Source:R/bold_data.R
get_bold_data.Rdget_bold_data uses taxon names from a tree topology, a character
vector of names or a datelifeQuery object, to search for genetic markers
in the Barcode of Life Database (BOLD).
Usage
get_bold_data(
input = c("Rhea americana", "Struthio camelus", "Gallus gallus"),
marker = "COI",
...
)Arguments
- input
One of the following:
- A character vector
With taxon names as a single comma separated starting or concatenated with
c().- A phylogenetic tree with taxon names as tip labels
As a
phyloormultiPhyloobject, OR as a newick character string.- A
datelifeQueryobject An output from
make_datelife_query().
- marker
A character vector indicating the gene from BOLD system to be used for branch length estimation. It searches "COI" marker by default.
- ...
Arguments passed on to
get_otol_synthetic_treeotol_versionVersion of Open Tree of Life to use
resolveDefaults to
TRUE. Whether to resolve the tree at random or not.ott_idsIf not NULL, it takes this argument and ignores input. A numeric vector of ott ids obtained with
rotl::taxonomy_taxon_info()orrotl::tnrs_match_names()ortnrs_match().
Value
A phylo object. If there are enough BOLD sequences available for the
input taxon names, the function returns a tree with branch lengths proportional
to relative substitution rate. If not enough BOLD sequences are available
for the input taxon names, the function returns the topology given as
input, or a synthetic Open Tree of Life for the taxon names given in
input, obtained with get_otol_synthetic_tree().