ncbi-taxonomy 开源项目推荐（45 个）

zyxue /ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

bio4j /bio4j

Bio4j 抽象模型及项目的通用入口点

seqan /lambda

LAMBDA – the Local Aligner for Massive Biological DatA

FOI-Bioinformatics /flextaxd

FlexTaxD（灵活分类数据库）——创建、添加、合并不同的分类源（QIIME、GTDB、NCBI 等）并创建宏基因组数据库（如 kraken2、ganon 等）

oganm /homologene

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

HadrienG /taxadb

🐣 locally query the ncbi taxonomy

obophenotype /ncbitaxon

Build for NCBITaxon

shenwei356 /taxid-changelog

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

oganm /geneSynonym

Quick access to gene synonyms

Joseph7e /Assign-Taxonomy-with-BLAST

可以使用BLAST算法来分配分类标签，这种方法适用于qiime工具中。

guyleonard /taxdump_edit

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

banhbio /Taxonomy.jl

Julia package to handle the NCBI Taxonomy database.

tetsufmbio /taxallnomy

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

pmenzel /taxonomy-tools

C++ tools for NCBI taxonomy tasks

PoisotLab /NCBITaxonomy.jl

Wrapper around the NCBI taxonomy files

Grelot /global_fish_genetic_diversity

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

pcantalupo /annotater

Annotate sequences by BLAST using NCBI taxonomy information

tetsufmbio /taxontree

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

ggonnella /fastsubtrees

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.

CVUA-RRW /taxidtools

Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files