Coordinate systemes in genomics (https://juke34.github.io/coordinate_systems/)

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

Code to compute the XP-CLR statistic to infer natural selection

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

predicting DFE and alpha from polymorphism data

modified version of scrm where self-fertilization and seed bank have been intergrated

A python3 package for operations on pedigree and genotype data

Infer a tree sequence from genetic variation data.

Extra add-ons that may be useful for people using SLiM, but that are not part of the SLiM project itself

GONE: Scripts, programs and an example data set

Useful bioinformatic scripts

Software for painlessly estimating average nucleotide diversity within and between populations

A python script for estimate the Inverse Instantaneous Coalescent Rate from coalescent times simulated with the ms software.

Coalescent Likelihood Under Effects of Selection - Inferring selection & allele frequency trajectories from nucleotide data

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

deep learning prediction of geographic location from individual genome sequences

No non-sense and no BS repo for how data structure code should be in Python - simple and elegant.

Tools for dealing with tree sequences coming to and from SLiM.

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

Segmented HAPlotype Estimation and Imputation Tool

Quantifying Introgression via Branch Lengths

A fast topological recombination estimator

A toolkit for analyzing and visualizing phylogenetic (placement) data

Sweep Inference Framework (controlling for correlation)

Genotyping Uncertainty with Sequencing data - Linkage Disequilibrium

Estimating evolutionary coevality

Command-line tool that instantly fetches Stack Overflow results when an exception is thrown