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  1. SpacerPlacer SpacerPlacer Public

    ancestral reconstruction and likelihood analysis for CRISPR spacer arrays

    Python 11 2

  2. goldfinder goldfinder Public

    Goldfinder detects gene co-occurrence and avoidance accounting for phylogenetic relationships

    Jupyter Notebook 11

  3. AIMsetfinder AIMsetfinder Public

    AIMsetfinder is a collection of Rscripts to identify sets of Ancestry Informative Markers (AIMs), that minimize the logloss error of a naive Bayes classifier.

    R 4 2

  4. ML-PopGen-Tutorials ML-PopGen-Tutorials Public

    Jupyter Notebook 3 1

  5. panicmage panicmage Public

    panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.

    C++ 2 1

  6. phylothin phylothin Public

    A coalescent theory based tool to identify oversampling in prokaryotic strain collections

    C 2 1