Download an alignment, sequence, or tree file from the ToL SFTP server.
download_tol(download_link = NULL, save_dir = NULL)A string specifying the URL to download the file from.
You can get a download URL for a particular specimen or gene using lookup_tol().
A string specifying the folder to save the download in. If no value is provided, here will be used.
The Tree of Life is a database of specimens sequenced as part of Kew's efforts to build a comprehensive evolutionary tree of life for flowering plants.
Sequence, alignment, and Newick tree files are help on an SFTP server
for download. The URLs to access these are stored in entries for specimens
and genes in the ToL database. These can be accessed by either using search_tol()
to get all specimens for a particular order, family, genus, or species or by
looking up a specific specimen or gene using lookup_tol()
Baker W.J., Bailey P., Barber V., Barker A., Bellot S., Bishop D., Botigue L.R., Brewer G., Carruthers T., Clarkson J.J., Cook J., Cowan R.S., Dodsworth S., Epitawalage N., Francoso E., Gallego B., Johnson M., Kim J.T., Leempoel K., Maurin O., McGinnie C., Pokorny L., Roy S., Stone M., Toledo E., Wickett N.J., Zuntini A.R., Eiserhardt W.L., Kersey P.J., Leitch I.J. & Forest F. 2021. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Systematic Biology, 2021; syab035, https://doi.org/10.1093/sysbio/syab035
lookup_tol() to lookup information about a sequenced specimen
using a valid ToL ID.
search_tol() to search ToL using taxonomic info.
load_tol() load a file from the ToL SFTP server.
Other ToL functions:
load_tol(),
lookup_tol()
if (FALSE) {
# download a specimen fasta file
specimen_info <- lookup_tol("1296")
download_tol(specimen_info$fasta_file_url)
# download a gene alignment file
gene_info <- lookup_tol("51", type="gene")
download_tol(gene_info$alignment_file_url)
# download the gene tree
download_tol(gene_info$tree_file_url)
}