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bio610_popgen

Bio 610 module on population genetics

colab_wiki

diploshic

feature-based deep learning for the identification of selective sweeps

discoal

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

dispersenn

Estimating dispersal using deep neural networks

dispersenn2

estimating dispersal distance from georeferenced polymorphisms

filet

Software for detecting introgression using supervised machine learning

greatapes_sims

im_clam

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

locator

deep learning prediction of geographic location from individual genome sequences

mapnn

neural network for estimating demographic maps from SNPs

msutils

A collection of C utilities for working with ms-formatted output files. Code is fast, flexible, and has many stats implemented

popcons

constrained elements predicted from population genomic data

popgendl_crashcourse

popvae

genotype dimensionality reduction with a VAE

product-space-fem

relernn

Recombination Landscape Estimation using Recurrent Neural Networks

shic

The Soft/Hard Inference through Classification tool for detecting hard and soft selective sweeps

snakemake_example

snakemake workflow example for msprime

softshoulders

Contains supplementary data from the Schrider et al. (2015) "Soft Shoulders" paper.

spaceness

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data

spatial_sims_standard

standardizing spatial simulation slim scripts with a template

stairwayplotmisorient

Liu and Fu's StairwayPlot program modified to estimate a mispolarization parameter