Introduction | Requirements | Installation | Preparation | Assigning taxonomy | Producing accession numbers | Finding taxonomy for NCBI accession numbers | Finding taxonomy for taxonomic names | Finding descendants for a given taxa | Finding common names for taxonomic IDs | Condensing taxonomy a.k.a. lowest common ancestor LCA | Find all taxonomic assignments for a given taxa | Finding accessions for a given taxonomic ID | Convert taxonomy to Newick tree | Note: NCBI name changes in early 2023 | Changelog | v0.11.1 | v0.10.8 | v0.10.7 | v0.10.6 | v0.10.5 | v0.10.4 | v0.10.3 | v0.10.2 | v0.10.1 | v0.9.4 | v0.9.3 | v0.9.2 | v0.8.4 | v0.8.3 | v0.8.2 | v0.8.1 | v0.8.0 | v0.7.1 | v0.7.0 | v0.6.0 | v0.5.3 | v0.5.0 | Manual preparation of database (usually not necessary) | Download names and nodes | Download accession to taxa files | Convert names, nodes and accessions to database | Switch from data.table to SQLite