Author: Klara Kaleb
Date: 2025-10-31

# Exploring Taxonomic trees with OmaDB

#### Klara Kaleb

#### 2025-10-31

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)

    ## [1] "root_taxon : NULL"
    ## [1] "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.