get_bold_data: Get genetic data from the Barcode of Life Database (BOLD) for...

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names.

Description

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).

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 phylo or multiPhylo object, OR as a newick character string. A datelifeQuery object 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_tree otol_version Version of Open Tree of Life to use resolve Defaults to TRUE. Whether to resolve the tree at random or not. ott_ids If 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().

Details

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.

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().

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.