Tools to work with variant call format files

Recombination Landscape Estimation using Recurrent Neural Networks

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

An Efficient Swiss Army Knife for Population Genomic Analyses in R

rhierbaps: R implementation of hierBAPS

Population-wide Deletion Calling

Estimation of population genetic parameters using deep learning

Genome-wide scan for balancing selection using beta statistic

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

PyPop: Python for Population Genomics

the hierfstat package

Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

Upscaling SV detection to a multi-population level.

群体遗传学分析中用到的script和skill等

A tool to visualize the haplotype pattern and various information in excel.

Python package for detecting positive selective sweeps using time-series genomics sampling data.

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Automated and Distributed Population Genetic Model Inference from Allele Frequency Spectra

The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049