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    29 repositories

    • popgensbi_snakemake

      Public
      Snakemake workflow for popgensbi
      Jupyter Notebook
      •
      MIT License
      •1•0•3•2•Updated Jul 31, 2025Jul 31, 2025

    • ReLocator

      Public
      modular API for genetic geolocation using deep neural networks (i.e. version 2 of locator)
      Jupyter Notebook
      •
      Other
      •1•1•0•0•Updated Jul 23, 2025Jul 23, 2025

    • discoal

      Public
      discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples
      recombinationsimulation-modeladmixture-eventsselective-sweepsdemographic-changes
      TeX
      •
      GNU General Public License v3.0
      •10•50•2•0•Updated Jun 25, 2025Jun 25, 2025

    • cxt

      Public
      Coalescence X Translation
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 23, 2025Jun 23, 2025

    • mapNN

      Public
      neural network for estimating demographic maps from SNPs
      Python
      •
      MIT License
      •1•11•3•0•Updated Jun 4, 2025Jun 4, 2025

    • diploSHIC

      Public
      feature-based deep learning for the identification of selective sweeps
      cnnpopulation-geneticsselective-sweepsdeep-learningtensorflow
      Python
      •
      MIT License
      •16•57•7•2•Updated Jun 3, 2025Jun 3, 2025

    • ReLERNN

      Public
      Recombination Landscape Estimation using Recurrent Neural Networks
      deep-learningrecurrent-neural-networkspopulation-genomicsrecombination
      Python
      •
      MIT License
      •11•58•5•0•Updated Apr 2, 2025Apr 2, 2025

    • relernn_nextflow

      Public
      Nextflow pipeline to run ReLERNN
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • popvae

      Public
      genotype dimensionality reduction with a VAE
      Python
      •
      Other
      •9•46•3•2•Updated Mar 11, 2025Mar 11, 2025

    • disperseNN2

      Public
      estimating dispersal distance from georeferenced polymorphisms
      deep-learningpopulation-geneticsdispersal
      Python
      •
      MIT License
      •2•4•7•0•Updated Mar 4, 2025Mar 4, 2025

    • spatial_sweeps

      Public
      HTML
      •0•1•0•0•Updated Feb 10, 2025Feb 10, 2025

    • locator

      Public
      deep learning prediction of geographic location from individual genome sequences
      deep-learninggeographypopulation-genetics
      Python
      •
      Other
      •16•51•8•2•Updated Jan 20, 2025Jan 20, 2025

    • msUtils

      Public
      A collection of C utilities for working with ms-formatted output files. Code is fast, flexible, and has many stats implemented
      C
      •
      MIT License
      •1•1•0•0•Updated Dec 13, 2024Dec 13, 2024

    • barnacle_simulation

      Public
      We are building a biologically and ecologically realistic SLiMulation of barnacles.
      Slim
      •0•2•0•0•Updated Nov 15, 2024Nov 15, 2024

    • spatial_sims_standard

      Public
      standardizing spatial simulation slim scripts with a template
      Jupyter Notebook
      •1•6•0•3•Updated Oct 4, 2024Oct 4, 2024

    • greatapes_sims

      Public
      Jupyter Notebook
      •0•1•2•0•Updated Oct 5, 2023Oct 5, 2023

    • disperseNN

      Public
      Estimating dispersal using deep neural networks
      Python
      •3•7•0•0•Updated Sep 29, 2023Sep 29, 2023

    • product-space-FEM

      Public
      Jupyter Notebook
      •2•2•4•0•Updated Aug 9, 2023Aug 9, 2023

    • popgenDL_crashcourse

      Public
      HTML
      •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

    • FILET

      Public
      Software for detecting introgression using supervised machine learning
      C
      •
      GNU General Public License v3.0
      •5•21•1•0•Updated Nov 21, 2022Nov 21, 2022

    • bio610_popgen

      Public
      Bio 610 module on population genetics
      Jupyter Notebook
      •0•0•2•0•Updated Mar 11, 2022Mar 11, 2022

    • colab_wiki

      Public
      2•3•0•0•Updated Feb 24, 2021Feb 24, 2021

    • shIC

      Public
      The Soft/Hard Inference through Classification tool for detecting hard and soft selective sweeps
      C
      •0•15•1•0•Updated Feb 2, 2021Feb 2, 2021

    • spaceness

      Public
      Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
      HTML
      •3•7•0•0•Updated Apr 10, 2020Apr 10, 2020

    • snakemake_example

      Public
      snakemake workflow example for msprime
      Python
      •0•0•0•0•Updated Nov 1, 2019Nov 1, 2019

    • im_clam

      Public
      package for exact calculation of the joint site frequency spectrum under Isolation with Migration models as described in Kern and Hey (2017) http://www.genetics.org/content/207/1/241
      C
      •
      MIT License
      •0•2•1•0•Updated Nov 24, 2017Nov 24, 2017

    • stairwayPlotMisorient

      Public
      Liu and Fu's StairwayPlot program modified to estimate a mispolarization parameter
      Java
      •
      GNU Lesser General Public License v3.0
      •0•4•0•0•Updated Nov 29, 2016Nov 29, 2016

    • popCons

      Public
      constrained elements predicted from population genomic data
      1•0•0•0•Updated Oct 7, 2015Oct 7, 2015

    • softShoulders

      Public
      Contains supplementary data from the Schrider et al. (2015) "Soft Shoulders" paper.
      0•0•0•0•Updated Feb 6, 2015Feb 6, 2015