Taxonomy.jl

Stable Dev

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DOI

Taxonomy.jl is a julia package to handle NCBI-formatted taxonomic databases. The main features are:

  • Convert a name to taxids
  • Traverse taxonomic subtrees from a given taxon
  • Compute the lowest common ancestor (LCA) of given taxons
  • Evaluate ancestor/descendant relationships between two taxa
  • Filter taxa by 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