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@kussell-lab

Kussell Lab at New York University

We combine theoretical biophysical approaches with experiments and bioinformatics to explore systems that exhibit complex, population-level phenomena.

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  1. mcorr mcorr Public

    Inferring bacterial recombination rates from large-scale sequencing datasets.

    Go 41 8

  2. viral-mcorr viral-mcorr Public

    Using correlated substitutions to infer recombination rates in RNA viruses

    Go 17 1

  3. ReferenceAlignmentGenerator ReferenceAlignmentGenerator Public

    Mapping reads to the reference genome to construct consensus genomes and generate alignments

    Go 2 1

  4. popsimu popsimu Public

    A GO package for population simulation with horizontal gene transfer

    Go 1

  5. hgtlib hgtlib Public

    forward population simulations with selection and recombination

    C 1 1

  6. PangenomeAlignmentGenerator PangenomeAlignmentGenerator Public

    Align SRAs to pangenome FASTA file generated by Roary

    Go 1 1

Repositories

Showing 10 of 19 repositories
  • mcorr Public

    Inferring bacterial recombination rates from large-scale sequencing datasets.

    kussell-lab/mcorr’s past year of commit activity
    Go 41 8 6 1 Updated Feb 25, 2023
  • viral-mcorr Public

    Using correlated substitutions to infer recombination rates in RNA viruses

    kussell-lab/viral-mcorr’s past year of commit activity
    Go 17 Apache-2.0 1 0 0 Updated Jan 26, 2023
  • virus_alignment_example Public

    Example workflow for aligning viral genomes for use with viral-mcorr using sars-like coronaviruses

    kussell-lab/virus_alignment_example’s past year of commit activity
    Python 0 0 0 0 Updated Sep 15, 2022
  • viral-mcorr_sl-cov_examples Public

    Example workflows for using viral-mcorr to infer recombination rates for RNA viruses

    kussell-lab/viral-mcorr_sl-cov_examples’s past year of commit activity
    HTML 0 0 0 0 Updated Sep 15, 2022
  • ReferenceAlignmentGenerator Public

    Mapping reads to the reference genome to construct consensus genomes and generate alignments

    kussell-lab/ReferenceAlignmentGenerator’s past year of commit activity
    Go 2 1 0 0 Updated Sep 15, 2022
  • mcorr-clustering Public

    Hierarchical clustering using mcorr

    kussell-lab/mcorr-clustering’s past year of commit activity
    Go 0 0 0 0 Updated Oct 26, 2021
  • ecological-memory Public
    kussell-lab/ecological-memory’s past year of commit activity
    Mathematica 0 0 0 0 Updated Sep 16, 2021
  • PangenomeAlignmentGenerator Public

    Align SRAs to pangenome FASTA file generated by Roary

    kussell-lab/PangenomeAlignmentGenerator’s past year of commit activity
    Go 1 1 0 0 Updated Jun 25, 2021
  • Helicobacter_pylori_transformation_experiments Public

    An example for mcorr

    kussell-lab/Helicobacter_pylori_transformation_experiments’s past year of commit activity
    0 0 0 0 Updated Jun 12, 2018
  • Helicobacter_pylori_global_population Public

    An example for mcorr

    kussell-lab/Helicobacter_pylori_global_population’s past year of commit activity
    Python 0 1 1 0 Updated Jun 12, 2018
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