Brranching is an interface to many different sources of phylogenetic data (currently only from Phylomatic (http://phylodiversity.net/phylomatic/), but more sources to come) that allows users to query for phylogenetic data using taxonomic names.
For brranching::phylomatic_names() function you should get an NCBI Entrez API key. NCBI Entrez doesn’t require that you use an API key, but you get higher rate limit with a key, from 3 to 10 requests per second, so do get one. Run taxize::use_entrez() or see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ for instructions.
Stable CRAN version
Or dev version
taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
tree <- phylomatic(taxa=taxa, get = 'POST')
plot(tree, no.margin=TRUE)
You can pass in up to about 5000 names. We can use taxize to get a random set of plant species names.
library("taxize")
spp <- names_list("species", 200)
out <- phylomatic(taxa = spp, get = "POST")
plot(out, show.tip.label = FALSE)
brranching in R doing citation(package = 'brranching')