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admixinfer

Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

admixsim

Java Version for the AdmixSim: A Forward-Time Simulator for Various and Complex Scenarios of Population Admixture

admixsim2

forward-time simulator of population genetic data

admixture.merge

To merge the replicates of ADMIXTURE analysis and provide summary report.

ancestrypainter

AncestryPainter is a graphic program used to illuminate the ancestry compositions of populations and individuals.

ancestrypainterv2

An updated version of AncestryPainterV1, a graphing tool to display ancestry composition and genetic difference.

archaicseeker

ArchaicSeeker is a software to detect archaic-like haplotypes in non-African modern human.

archaicseeker2.0

ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following three notable improvements compared with the original version of this software. First, it can automatically determine the boundary of each introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.

asekit

A tool applied to detect allelic expression sites

calculate.genetic.distance

This script can calculate the genetic distances of given variants based on their physical positions and genetic map files.

camer

Continuous Admixture Modeler: R package for Continuous Admixture Modeling (CAMer)

chinese-pangenome-consortium-phase-i

chip-mutation-calling-ngs-pipeline

This pipeline based on snakemake calls CHIP variants from next-generation whole-exome/genome sequencing of human samples and produces a purely filtered VCF file containing high confident CHIP mutations.

construct-ancestral-genome

cpc-graph-based-ngs-pipeline

A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data

cvetool

Composite variant expression tool

genetic-characteristics-of-the-han100k-initiative

We calculated pairwise FST and Ancestry components for each provincial population.

herv-identification-and-calling-pipeline

hierarchymix

reconstruct the 4-way complex admixture history

imaaps

To infer multiple-wave admixture by fitting ALD using a p-spectrum

imaapssmry0.2

Version 0.2 of R package iMAAPssmry

multiwaver

Inference of multiple-wave admixtures by length distribution of ancestral tracks

multiwaver2.0

MultiWaver series software was designed to infer population admixture history in case of various and complex scenarios. The earlier version of MultiWaver considered only the discrete admixture models. In the newly developed version MultiWaver 2.0, we implemented a more flexible framework to automatically select an optimal admixture model among discrete models and continuous models.

multiwaverx

Inference on the sex-biased admixture history

ngs.prss1-2caller

NGS.PRSS1-2caller is a toolkit for calling genetic variants at PRSS1-PRSS2 locus, which enables detecting SNV, INDEL and CNV with high accuracy and sensitivity.

pangenome_vcf_postprocess

A simple pipeline to process the VCF deconstructed from the VG pangenome graph

peas

Package for Elementary Analysis for SNP data

pgg.mhc

pggsvpipeline

rna-seq