🐞 Convert NCBI taxonomy dump into lineages

Bio4j abstract model and general entry point to the project

LAMBDA – the Local Aligner for Massive Biological DatA

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

🐭 ↔️ 👫 An r package that works as a wrapper to homologene

🐣 locally query the ncbi taxonomy

NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.

Build for NCBITaxon

Quick access to gene synonyms

Assign taxonomy with blast, can be used for qiime

🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files

Julia package to handle the NCBI Taxonomy database.

C++ tools for NCBI taxonomy tasks

Taxallnomy is a balanced taxonomic tree database based on NCBI Taxonomy that provides taxonomic lineages according to the taxonomic ranks of Linnean classification system.

Codes I wrote for the paper : "Global determinants of freshwater and marine fish genetic diversity" Nature Communications, 2020

Wrapper around the NCBI taxonomy files

Annotate sequences by BLAST using NCBI taxonomy information

Python library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.

TaxOnTree is a bioinformatic tool that automatically colors a phylogenetic tree according to the taxonomic information provided by NCBI taxonomy.

GPT (Decoder only Transformer - from scratch) generated fake/phoney taxonomies (based on NCBI taxonomy dataset)