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    21 repositories

    • threads

      Public
      Scalable inference of ancestral recombination graphs
      C++
      •
      GNU General Public License v3.0
      •1•2•10•4•Updated Jan 29, 2026Jan 29, 2026

    • arg-needle

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • arg-lmm

      Public
      ARG-based linear mixed model analysis
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • arg-needle-lib

      Public
      ARG-Needle library for representing and analyzing ancestral recombination graphs (ARGs)
      C++
      •
      GNU General Public License v3.0
      •3•10•4•0•Updated Nov 21, 2025Nov 21, 2025

    • ASMC

      Public
      Ascertained Sequentially Markovian Coalescent
      C++
      •
      GNU General Public License v3.0
      •1•16•3•0•Updated Oct 22, 2025Oct 22, 2025

    • PrepareDecoding

      Public
      Tool to compute decoding quantities
      C++
      •
      GNU General Public License v3.0
      •0•0•1•1•Updated Sep 27, 2025Sep 27, 2025

    • quickdraws

      Public
      Python
      •
      GNU General Public License v3.0
      •1•11•2•0•Updated Aug 3, 2025Aug 3, 2025

    • HapNe

      Public
      Haplotype-based inference of recent effective population size in modern and ancient DNA samples
      Python
      •
      GNU General Public License v3.0
      •2•11•8•0•Updated Apr 4, 2025Apr 4, 2025

    • ARG-LMM_experiments

      Public
      Simulation and analysis scripts for Zhang et al. Nature Genetics, 2023
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • EpiNN_data

      Public
      MATLAB
      •0•1•0•0•Updated Nov 17, 2023Nov 17, 2023

    • EpiNN

      Public
      Python
      •0•1•0•0•Updated Nov 17, 2023Nov 17, 2023

    • coalNN_data

      Public
      Files needed for CoalNN experiments: genetic maps, demographies, UKBB allele frequencies.
      0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • coalNN

      Public
      Convolutional neural network for TMRCA and allele age inference.
      Python
      •2•4•0•0•Updated Sep 13, 2023Sep 13, 2023

    • arg-needle-scripts

      Public
      Python
      •1•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • ASMC_data

      Public
      Public data for use with ASMC
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 17, 2023Feb 17, 2023

    • DataModule

      Public
      Data module and utilities that will underpin other software from the Palamara Lab
      C++
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Jun 24, 2022Jun 24, 2022

    • OxStatGen22

      Public
      Computational Exercise for the Oxford 2022 Statistical Genetics Summer School
      Jupyter Notebook
      •0•0•0•0•Updated Jun 19, 2022Jun 19, 2022

    • ASMC_legacy

      Public
      Ascertained Sequentially Markovian Coalescent
      Java
      •
      GNU General Public License v3.0
      •9•4•12•0•Updated Sep 27, 2021Sep 27, 2021

    • 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 …
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•14•3•0•Updated Sep 2, 2021Sep 2, 2021

    • vcpkg-registry

      Public
      Registry for hosting C++ packages for installation via vcpkg
      CMake
      •
      MIT License
      •0•0•0•0•Updated Aug 31, 2021Aug 31, 2021

    • ARGON

      Public
      Fast, whole-genome simulation of the discrete time Wright-Fisher process
      Java
      •
      Apache License 2.0
      •3•0•0•0•Updated Nov 22, 2017Nov 22, 2017