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resource: AncestryPainter
description: AncestryPainter is a graphic program used to illuminate the ancestry compositions of populations and individuals in a way to save space with a rounded and nice-looking graph. It requires Perl and R software to run the program. It is user-friendly and many details in the graph could be handled with command lines (Please check the Manual for detailed information).
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resource: MultiWaver
description: MultiWaver is designed to scan the number of waves of admixture events, and estimate the parameters of admixture models with multi-waves, multi-ancestral populations via the length distribution of the ancestral tracks. The program works mainly in two steps: Firstly, use LRT and EM-algorithm to scan the number of waves for each ancestral population. Secondly, use the theoretical length distribution of ancestral tracks to estimate the parameters (i.e. the proportions and generations).
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resource: ArchaicSeeker
description: ArchaicSeeker, a program to detect archaic-like chromosomal segments in non-African modern human genomes.
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resource: iMAAPs
description: iMAAPs 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.
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resource: CAMer
description: CAMer package is a R package for inferring continuous admixture time interval, which is based on the result of iMAAPs. Related Publication: Modeling Continuous Admixture-------------------------- (doi: http://dx.doi.org/10.1101/026278)------------------------------------ Link: http://biorxiv.org/content/early/2015/09/08/026278
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resource: AdmixInfer v1.0.4
description: 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 ---------(doi: http://dx.doi.org/10.1101/023390) ----------------------------------------Link: http://biorxiv.org/content/early/2015/07/28/023390
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resource: AdmixSim-v1.0.2
description: 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.
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resource: WinXPCNVer
description: 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. -------------------------------------------------------------(doi: http://dx.doi.org/10.1016/j.ajhg.2015.05.005) ----------------------Link: http://www.cell.com/ajhg/abstract/S0002-9297%2815%2900191-3
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resource: SC (Spatial Coalescent simulator)
description: SC (Spatial Coalescent simulator) is a computer simulation tool for modeling spatial coalescent with recombination process. The algorithm implemented in SC is an improvement of the Wiuf and Hein algorithm (Wiuf and Hein, 1999). SC is proven to be the only precise ancestral recombination graph (ARG) simulator (Wiuf and Hein’s has some redundant and MaCS misses some information) such as the distribution of ARG generated by SC is identical to that generated by a typical back-in-time model adopted by ms. SC is developed based on Macs-0.4e, all macs options are not changed. Thanks to Gary Chen to provide support. ---------------------------------------------------Related Publication: A New Method for Modeling Coalescent Processes with Recombination.--------------------------------------------------------------------- (doi:10.1186/1471-2105-15-273) -----------------------------------------------Link: http://www.biomedcentral.com/1471-2105/15/273
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resource: SC-sample
description: SC-sample is a computer simulation tool for modeling spatial coalescent with recombination process, which generates ARGs directly consistent with the given sample. It attempts to uniformly select ARG from the sample-consistent ARG space. The algorithm is modified version of SC. -----------Related Publication: A New Method for Modeling Coalescent Processes with Recombination.-------------------------------------------------------------------- (doi:10.1186/1471-2105-15-273) ----------------------------------------------Link: http://www.biomedcentral.com/1471-2105/15/273
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resource: PEAS
description: Developed by Shuhua Xu. PEAS can handle very large data set, it is versatile especially in formatting, data splitting, data combining, sampling for both markers and individuals for further analysis. To fill up the gaps of currently available programs, PEAS are designed to calculate individual allele sharing distance, population genetic distances, do bootstrapping and calculating LD statistics for large-scale SNP data set. As the assistant tools of many other popular programs, PEAS are also designed to provide formatted input files for many programs, such as fastPHASE, PHASE, STRUCTURE, Haploview, Arlequin and LDhat and so on. PEAS can also manage the output results of some other programs. Here provide you a zip file including the entire package and package without GUI, the user guide file and the related paper.
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