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Taxonomy.jl is a julia package to handle the NCBI Taxonomy database. The main features are:

  • Get various information on a given taxon (name, rank, parent-child relationships, etc.)
  • Convert a name to Taxids
  • Traverse taxonomic subtrees from a given taxon
  • Compute the lowest common ancestor (LCA) of given taxa
  • Evaluate ancestor-descendant relationships between two taxa
  • Filter taxa by a rank range
  • Construct taxonomic lineage of the given taxon
  • Reformat lineage according to canonical ranks
  • Construct a DataFrame from lineages

Now, this package only supports scientific name.


Install Taxonomy.jl as follows:

julia -e 'using Pkg; Pkg.add("Taxonomy")'

Download database

You need to download taxonomic data from NCBI's servers.

tar xzvf taxdump.tar.gz