Repositories list

• 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 17, 2025Jul 17, 2025

• popgensbi_snakemake

  Public
  Snakemake workflow for popgensbi

  Jupyter Notebook

  •

  MIT License

  •1•0•3•2•Updated Jul 16, 2025Jul 16, 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-events+ 2selective-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-sweeps+ 2deep-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-genomics+ 1recombination

  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

  •17•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