Using OmaDB, a user can easily obtain a taxonomic tree of interest using the getTaxonomy structure. The tree can be restricted to a certain root or by a list of members and the data is returned in the newick format. The newick can then be exported and used to create a tree object using ape which can then be visualised using ggtree.
This is done below using the getTaxonomy(root=‘Alveolata’) function, the output of which is below.
library(OmaDB) load('../data/taxonomy.rda') getObjectAttributes(taxonomy)
##  "root_taxon : NULL" ##  "newick : character"
The tree can be further analysed and annotated using the ggtree package also available in Bioconductor. This can easily be done using the getTree() function in OmaDB.