Taxonomy.jl

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.

Installation

Install Taxonomy.jl as follows:

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

Download database

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

wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar xzvf taxdump.tar.gz