Skip to content
Change the repository type filter

All

    Repositories list

    • Vue
      12110Updated Dec 5, 2024Dec 5, 2024
    • Toolkit for updating the GTDB to the next release and generating data files for the GTDB website.
      Python
      GNU General Public License v3.0
      1100Updated Dec 3, 2024Dec 3, 2024
    • GTDBTk

      Public
      GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
      Python
      GNU General Public License v3.0
      82488190Updated Dec 2, 2024Dec 2, 2024
    • Toolkit for establishing, updating, and validating GTDB species clusters
      Python
      Other
      32000Updated Nov 18, 2024Nov 18, 2024
    • Toolkit for updating the GTDB to the next release and test data
      Python
      0110Updated Oct 11, 2024Oct 11, 2024
    • Python
      GNU General Public License v3.0
      0300Updated Sep 3, 2024Sep 3, 2024
    • CheckM

      Public
      Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
      Python
      GNU General Public License v3.0
      73351181Updated Sep 3, 2024Sep 3, 2024
    • XSLT
      0000Updated Feb 23, 2024Feb 23, 2024
    • Automatic pre-curation of GTDB trees.
      Python
      GNU General Public License v3.0
      0000Updated Dec 12, 2023Dec 12, 2023
    • GTDBNCBI

      Public
      The GTDB provides the software infrastructure for working with a large collection of genomic resources. The major goal of this initiative is to provide a phylogenetically consistent taxonomy for archaea and bacteria.
      Python
      GNU General Public License v3.0
      29170Updated Oct 30, 2023Oct 30, 2023
    • gtdb-lib

      Public
      An abstraction of objects, files, and third-party tools used by the GTDB. Not intended for public use.
      Python
      GNU General Public License v3.0
      0000Updated Apr 17, 2023Apr 17, 2023
    • Creates iTOL files for tree decoration, given a set of GTDB genomes.
      Python
      GNU General Public License v3.0
      0440Updated Nov 3, 2022Nov 3, 2022
    • GTDB database service
      Shell
      0000Updated May 27, 2022May 27, 2022
    • hatchet

      Public
      Tools used to split the GTDB-Tk reference tree into smaller sub trees
      Python
      0100Updated May 16, 2022May 16, 2022
    • A template for distributing jobs across the ACE cluster.
      Python
      GNU General Public License v3.0
      0100Updated Mar 8, 2022Mar 8, 2022
    • slamM

      Public
      slamM: a hybrid metagenomic assembly pipeline
      Python
      GNU General Public License v3.0
      0100Updated Mar 10, 2021Mar 10, 2021
    • ace-conda

      Public
      ACE specific conda configuration packages.
      Shell
      0000Updated Mar 2, 2021Mar 2, 2021
    • DeltaPD

      Public
      DeltaPD is a tool used to determine outliers in a gene tree when compared against a reference tree.
      Python
      GNU Affero General Public License v3.0
      0000Updated Dec 2, 2020Dec 2, 2020
    • scripts

      Public
      Public scripts referenced in ACE manuscripts
      Python
      GNU General Public License v3.0
      0000Updated Mar 26, 2020Mar 26, 2020
    • ace-guix

      Public
      GNU Guix package definitions for ACE or otherwise
      Scheme
      GNU General Public License v3.0
      1200Updated Nov 23, 2019Nov 23, 2019
    • BamM

      Public
      Metagenomics-focused BAM file manipulation
      C
      GNU Lesser General Public License v3.0
      716120Updated Jul 8, 2019Jul 8, 2019
    • Download project fastq files from BaseSpace
      Python
      0311Updated Nov 13, 2017Nov 13, 2017
    • mingle

      Public
      Australian Centre for Ecogenomics' genome tree database: Taxonomically annotated trees from HMMs and BLAST
      Python
      GNU General Public License v3.0
      2241Updated May 13, 2017May 13, 2017
    • Script for downloading data from ACE Sequencing
      Python
      0000Updated Feb 2, 2017Feb 2, 2017
    • gtdblib

      Public
      Python
      GNU General Public License v3.0
      1000Updated Nov 29, 2016Nov 29, 2016
    • GTDBLite

      Public archive
      Python
      4090Updated Oct 29, 2015Oct 29, 2015
    • pfam_scan meets hmmsearch.
      Perl
      2100Updated Sep 17, 2015Sep 17, 2015
    • ScaffoldM

      Public
      scaffoldm
      Python
      GNU General Public License v3.0
      0200Updated May 21, 2015May 21, 2015
    • APP

      Public archive
      Ace Pyrotag Pipeline - wrapper for QIIME and R - interfaces with PyroDB
      Perl
      30110Updated Apr 4, 2014Apr 4, 2014
    • PhylogeneticM

      Public archive
      Feed the tree...
      Python
      1110Updated Mar 11, 2013Mar 11, 2013