make_bold_otol_tree takes taxon names from a tree topology or
a vector of names to search for genetic markers in the Barcode of Life Database
(BOLD), create an alignment, and reconstruct branch lengths on a tree topology
with Maximum Likelihood.
make_bold_otol_tree(
input = c("Rhea americana", "Struthio camelus", "Gallus gallus"),
marker = "COI",
otol_version = "v3",
chronogram = TRUE,
doML = FALSE,
aligner = "muscle",
...
)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.
Version of Open Tree of Life to use
Default to TRUE, branch lengths returned are estimated with
ape::chronoMPL(). If FALSE, branch lengths returned are estimated with
phangorn::acctran() and represent relative substitution rates.
Default to FALSE. If TRUE, it does a ML branch length optimization
with phangorn::optim.pml().
A character vector indicating whether to use MAFFT or MUSCLE
to align BOLD sequences. It is not case sensitive. Default to MUSCLE,
supported using the msa
package from Bioconductor, which needs to be installed using BiocManager::install().
Arguments passed on to get_otol_synthetic_tree
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.