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resource: SimAncestry 1.0
description: SimAncestry is a script to extract archaic introgressed sequences from ms simulation output. The script SimAncestry is only a simple script to analyze the tree structure outputted by the software ms. It cannot be applied to the real data as it was not designed to work with SNP data. The algorithm used in SimAncestry is as follows. For each non-African node, we make a transversal up to the root. If this node coalesces to archaic lineage before any African lineages, we say this node is introgressed. This script is used only to obtain the ground truth for introgressed sequences.
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resource: Y-LineageTracker
description: Y-LineageTracker provides a framework to fully analyze human Y-chromosome sequencing data. Y-LineageTracker supports most of analyses of Y-chromosome sequencing data and facilitates subsequent studies of NRY haplogroups and Y-STRs. In brief, analyses of NRY haplogroup include haplogroup classification, clustering, phylogeny construction and estimating divergence time of haplogroups, and analyses of Y-STR include Y-STR genotyping, statistical analysis, network analysis and estimating TMRCA of Y-STR haplotypes.
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resource: ArchaicSeeker2.0
description: 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.
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resource: AdmixSim2
description: AdmixSim 2 is an individual-based forward-time simulation tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. It is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation. AdmixSim 2 can be used to simulate data of dioecious or monoecious populations, autosomes, or sex chromosomes. We have developed Cpp and Python version for AdmixSim 2.
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resource: MultiWaver 2.0
description: 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.------------------------------------ Related Publication: European Journal of Human Genetics. 27:133-139. Link:
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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). Related Publication: Genomics Proteomics Bioinformatics. 16(5):382-385. Link:
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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).-------------------------------------Related Publication: Heredity. 121:52-63. Link:
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resource: ArchaicSeeker
description: ArchaicSeeker, a program to detect archaic-like chromosomal segments in non-African modern human genomes.------------------------------------------Related Publication: Am.J.Hum.Genet. 99:580-594. Link:
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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.-------------------------------------------------------------------------Related Publication: Heredity. 118(5):503-510. Link:
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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-------------------------------------------------Related Publication: Scientific Reports. 7:43054. Link:
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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: Scientific Reports. 6:20048. Link:
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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: Am.J.Hum.Genet. 97(1):54-66. Link:
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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: BMC Bioinformatics. 15:273. Link:
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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: BMC Bioinformatics. 15:273. Link:
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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.-Related Publication: Mol.Ecol.Res. 10(6):1085-1088. Link:
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