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  • SPARSE Public

    Strain Prediction and Analysis with Representative SEquence

    C++ 18 4 GNU General Public License v3.0 Updated Dec 8, 2024
  • EToKi Public

    all methods related to Enterobase

    Python 39 18 GNU General Public License v3.0 Updated Sep 4, 2024
  • KleTy Public

    KleTy: Klebsiella genotyping for its core genome and plasmids

    Python 5 2 GNU General Public License v3.0 Updated Jul 4, 2024
  • StrTrak Public

    StrTrak: Strain Tracker for metagenomic data

    Python 3 2 GNU General Public License v3.0 Updated Jan 13, 2024
  • pHierCC Public

    Hierarchical clustering of cgMLST

    Python 11 5 GNU General Public License v3.0 Updated Nov 20, 2023
  • redHMM Public

    RecHMM + DivHMM, identification of recombination and diversifying selection in bacterial genomes

    Python 1 GNU General Public License v3.0 Updated Oct 27, 2023
  • cgMLSA Public

    Python 1 GNU General Public License v3.0 Updated Oct 7, 2023
  • 1 GNU General Public License v3.0 Updated Mar 28, 2023
  • EPHI Public

    Efficient Population History Inference

    Python Updated Dec 26, 2022
  • zscripts Public

    Python Updated Dec 13, 2022
  • SRAdownload Public

    A simple tool that downloads SRA short reads from either NCBI or EBI and converts them into fastq.gz files

    Python GNU General Public License v3.0 Updated May 31, 2022
  • rapidNJ Public

    Forked from somme89/rapidNJ

    Fast implementation of the Neighbour-Joining method for phylogenetic inference

    C++ GNU General Public License v2.0 Updated Feb 10, 2022
  • BioData Public

    Forked from bjtully/BioData

    All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

    Python MIT License Updated Aug 31, 2021
  • PhageBoost Public

    Forked from ku-cbd/PhageBoost

    Rapid discovery of novel prophages using biological feature engineering and machine learning

    Jupyter Notebook GNU General Public License v3.0 Updated Jul 27, 2021
  • public_kssd Public

    Forked from yhg926/public_kssd

    K-mer substring space decomposition

    C Other Updated Jun 10, 2021
  • Updated Feb 12, 2021
  • biopython Public

    Forked from biopython/biopython

    Official git repository for Biopython (originally converted from CVS)

    Python Other Updated Dec 26, 2020
  • PEPPAN Public

    Phylogeny Enhanded Prediction of PAN-genome

    Python 40 10 GNU General Public License v3.0 Updated Jul 17, 2020
  • misc Public

    Updated Jul 13, 2020
  • kmer-db Public

    Forked from refresh-bio/kmer-db
    C++ GNU General Public License v3.0 Updated Jul 1, 2020
  • BlastFrost Public

    Forked from nluhmann/BlastFrost
    C++ GNU General Public License v3.0 Updated Jun 27, 2020
  • fastSource Public

    Accurate classification of bacterial source metadata based on FastText

    Python GNU General Public License v3.0 Updated Jun 22, 2020
  • GrapeTree Public

    Forked from achtman-lab/GrapeTree
    JavaScript GNU General Public License v3.0 Updated Jun 8, 2020
  • PEPPAN_data Public

    Updated May 21, 2020
  • SimPan Public

    A simulator of pan-genome for bacterial population

    Python 3 GNU General Public License v3.0 Updated May 21, 2020
  • 1 Updated May 8, 2020
  • Use BlastFrost to identify QRDR SNPs

    Python GNU General Public License v3.0 Updated Feb 21, 2020
  • A simple script that can efficiently cluster divergent amino acid sequences based on the coverage of their alignments

    Python GNU General Public License v3.0 Updated Nov 25, 2019
  • metaParser Public archive

    Assign metadata into defined categories

    Updated Dec 13, 2018
  • The script is designed as part of the supplementary data for the manuscript: https://www.biorxiv.org/content/early/2017/02/03/105759

    Python Updated Jan 30, 2018