gtdb

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

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

GTDB taxonomy taxdump files with trackable TaxIds

A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

CLI tool for querying the Genome Taxonomy Database (GTDB). Batch search, genome cards, taxon lineages, and cross-release taxonomic comparison. JSON · CSV · TSV · stdin · parallel pagination · no runtime dependencies.

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

Mapping NCBI Genbank accession to GTDB accession

Benchmarking various taxonomic classifiers for profiling soil metagenomic data, with scripts and tools tailored for fungal, bacterial, and archaeal genome identification.

Protal is tool for taxonomic profiling from whole-genome shotgun sequencing data. With GTDB marker genes as reference, protal is able to cover most described bacteria. Protal is further able to disentangle intraspecific variation across samples.

A tool for phlyo tree, a phylogenetic tree construction software.

https://gtdb.ecogenomic.org/ gro.cimoИegoce.dbtg

A library for parsing Newick format files, especially GTDB tree files.

Align and merge NCBI Taxonomy and GTDB into a unified, consistent OWL knowledge graph (with optional iNaturalist common names).