🐞 Convert NCBI taxonomy dump into lineages

• UpdatedApr 4, 2022
• Python

Bio4j abstract model and general entry point to the project

• UpdatedDec 16, 2016
• Java

LAMBDA – the Local Aligner for Massive Biological DatA

• UpdatedAug 26, 2024
• C++

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

• UpdatedMar 12, 2025
• Python

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

• UpdatedNov 2, 2023
• R

🐣 locally query the ncbi taxonomy

• UpdatedDec 8, 2022
• Python

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

• UpdatedNov 20, 2024
• R

Build for NCBITaxon

• UpdatedMar 17, 2025
• Python

Quick access to gene synonyms

• UpdatedMar 16, 2025
• R

Assign taxonomy with blast, can be used for qiime

• UpdatedAug 18, 2023
• Python

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

• UpdatedMar 9, 2020
• Perl

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

• UpdatedMar 20, 2025
• Perl

Julia package to handle the NCBI Taxonomy database.

• UpdatedMar 11, 2025
• Julia

C++ tools for NCBI taxonomy tasks

• UpdatedJan 13, 2022
• C++

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

• UpdatedFeb 10, 2020
• R

Wrapper around the NCBI taxonomy files

• UpdatedMar 12, 2025
• Julia

Annotate sequences by BLAST using NCBI taxonomy information

• UpdatedJul 27, 2022
• Perl

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.

• UpdatedFeb 17, 2025
• Python

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

• UpdatedAug 24, 2022
• Perl

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

• UpdatedSep 10, 2023
• Jupyter Notebook