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
DataFramefrom lineages
Now, this package only supports scientific name.
Install Taxonomy.jl as follows:
julia -e 'using Pkg; Pkg.add("Taxonomy")'
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