[1] 估计群体重组率的软件 FastEPRR（软件下载）

下载包 FastEPRR.tar.gz，包括 FastEPRR_1.0.tar.gz (Linux/Unix安装版本), FastEPRR_1.0.zip (Windows安装版本) 和 FastEPRR_manual.pdf (用户手册)。

详细介绍和课题组信息可以访问----相关信息

[2] 进化树修饰工具 ItreeV （软件下载）

下载包 ItreeV.tar.gz，包括 Itree.jar (主程序)， ItreeV.bat (Windows下运行文件)， ItreeV.sh (Linux/Unix 下运行文件) , ItreeV_manual.pdf (用户手册)， examples 文件夹 (示例输入) 和 Readme 文件。

[3] MALDmef （软件下载）

MALDmef is a powerful tool to estimate multiple-wave population admixed time, which is currently designed to infer the two-way, multiple-wave admixture based on admixture induced LD. This software can deal with genotype data, haplotype data and the data re-coded according to admixture ancestries.

Related Publication: Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions

[4] CAMer （软件下载）

CAMer package (Continuous Admixture Modeler) does Continuous Admixture Modeling (CAM) and related summary based on the result of MALDmef.

Related Publication: Modeling Continuous Admixture

[5] AdmixInfer v1.0.4 （软件下载）

AdmixInfer is designed to optimize the parameters of admixture model via maximum likelihood estimation and figure out the model best fit the data. The optimization is under assumption of HI (Hybrid Isolation), GA(Gradual Admixture), CGFR (Continuous Gene Flow Recipient) and CGFD (Continuous Gene Flow Donor) model.

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

[6] AdmixSim-v1.0.2 （软件下载）

1.Population model assumptions The population in each generation evolves following standard Wright Fisher model without mutation and selection. That is, randomly sample two individuals from the population, and randomly choose one of the chromosomes in each individual, pair and recombine them to form a new chromosome pair for the next generation. Repeat this process until sampling N chromosome pairs. Here N denotes population size in specific generation. Recombination is modeled as Poisson Process along the chromosome with rate 1 (Unit in Morgan).

2. AdmixSim description Here we implemented a very flexible simulator for admixed population, in which: 1) Can take arbitrary number of ancestral populations; 2) Can take arbitrary waves of population admixture; 3) Population size can be changed generation by generation; 4) And admixture proportions can also be changed generation by generation.

[7] WinXPCNVer （软件下载）

WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.

Related Publication: A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence

[8] Du for detecting recent positive selection （软件下载 Windows Linux）

Currently, the Du program supports the fourpopularly used alignmentformat (ARLEQUIN, MEGA, NEXUS and PHYLIP). Please see the examples for the data format.

Related Publication: Statistical test for detecting recent positive selectionby partitioning coalescent tree (under publishing)