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PalamaraLab

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  1. ASMC ASMC Public

    Ascertained Sequentially Markovian Coalescent

    C++ 16 1

  2. FastSMC FastSMC Public

    FastSMC is a method to quickly and accurately estimate pairwise identical-by-descent (IBD) regions in the genome. FastSMC estimates the age of IBD segments and scales to large biobank datasets. htt…

    Jupyter Notebook 14 1

  3. quickdraws quickdraws Public

    Python 12

  4. arg-needle-lib arg-needle-lib Public

    ARG-Needle library for representing and analyzing ancestral recombination graphs (ARGs)

    C++ 9 2

  5. HapNe HapNe Public

    Haplotype-based inference of recent effective population size in modern and ancient DNA samples

    Python 8 2

  6. ASMC_legacy ASMC_legacy Public

    Ascertained Sequentially Markovian Coalescent

    Java 4 9

Repositories

Showing 10 of 19 repositories
  • arg-needle-lib Public

    ARG-Needle library for representing and analyzing ancestral recombination graphs (ARGs)

    PalamaraLab/arg-needle-lib’s past year of commit activity
    C++ 9 GPL-3.0 2 4 0 Updated May 9, 2025
  • threads Public

    Scalable inference of ancestral recombination graphs

    PalamaraLab/threads’s past year of commit activity
    C++ 1 GPL-3.0 0 6 1 Updated May 1, 2025
  • HapNe Public

    Haplotype-based inference of recent effective population size in modern and ancient DNA samples

    PalamaraLab/HapNe’s past year of commit activity
    Python 8 GPL-3.0 2 8 0 Updated Apr 4, 2025
  • ARG-LMM_experiments Public

    Simulation and analysis scripts for Zhang et al. Nature Genetics, 2023

    PalamaraLab/ARG-LMM_experiments’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Apr 2, 2025
  • quickdraws Public
    PalamaraLab/quickdraws’s past year of commit activity
    Python 12 GPL-3.0 0 1 0 Updated Mar 27, 2025
  • ASMC Public

    Ascertained Sequentially Markovian Coalescent

    PalamaraLab/ASMC’s past year of commit activity
    C++ 16 GPL-3.0 1 3 0 Updated Nov 21, 2024
  • EpiNN_data Public
    PalamaraLab/EpiNN_data’s past year of commit activity
    MATLAB 1 0 0 0 Updated Nov 17, 2023
  • EpiNN Public
    PalamaraLab/EpiNN’s past year of commit activity
    Python 1 0 0 0 Updated Nov 17, 2023
  • coalNN_data Public

    Files needed for CoalNN experiments: genetic maps, demographies, UKBB allele frequencies.

    PalamaraLab/coalNN_data’s past year of commit activity
    0 0 0 0 Updated Oct 31, 2023
  • coalNN Public

    Convolutional neural network for TMRCA and allele age inference.

    PalamaraLab/coalNN’s past year of commit activity
    Python 4 1 0 0 Updated Sep 13, 2023
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