get_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).
get_bold_data(
input = c("Rhea americana", "Struthio camelus", "Gallus gallus"),
marker = "COI",
...
)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().
One of the following:
With taxon names as a single comma separated
starting or concatenated with c().
As a phylo or
multiPhylo object, OR as a newick character string.
datelifeQuery objectAn output from make_datelife_query().
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_tree
otol_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() or
rotl::tnrs_match_names() or tnrs_match().
If input is a phylo object or a newick string, it is used as backbone topology.
If input is a character vector of taxon names, an induced synthetic OpenTree
subtree is used as backbone.