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.
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
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)
brranchingin R doing
citation(package = 'brranching')
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