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Structure 2.3.XThe program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPs, microsatellites, RFLPs and AFLPs. The basic algorithm was described by Pritchard, Stephens & Donnelly (2000). Extensions to the method were published by Falush, Stephens and Pritchard (2003), and (2007) and Hubisz, Falush, Stephens and Pritchard (2009).
TreeMix: estimation of population trees with admixtureTreeMix uses large numbers of SNPs to estimate the historical relationships among populations, using a graph representation that allows both population splits and migration events. You can download the TreeMix paper by Pickrell and Pritchard (2012) here.
CENTIPEDE: software for inference of TF binding sitesCENTIPEDE is a method developed by Roger Pique-Regi and Jacob Degner that uses PWM information plus experimental data such as DNase1, histone marks or FAIRE to infer transcription factor binding sites with high specificity. Software and data are available here.
Transcriptome AssemblerSoftware for transcriptome assembly used in RNA-seq of 16 mammalian species.Download assembler. BFCounter: Memory efficient k-mer countingBFCounter is a program for counting k-mers from DNA sequencing data it uses a Bloom filter data structure to filter unique k-mers, likely generated from sequencing errors. This is preliminary version, and should be updated soon.BFCounter Homepage Analysis and modeling of natural selectionScripts for computing two test statistics for detecting positive selection (iHS and XP-EHH), as well as a flexible tool for performing Wright-Fisher simulations with selection can be found here. (Note that data from our selection scans in humans [Voight et al 2006 and Pickrell et al 2009] can be found here and here, respectively.)Two programs written by Graham Coop when he was in the lab: one for simulating sweeps on standing variation and one for testing for correlations between allele frequencies and environmental variables can be obtained via Graham's website at UC Davis. Software for RNA-seq analysis, eQTLs, etcSome of the software that we have developed for analyzing RNA-seq data, including programs for counting reads, de novo identification of splice junctions, and detection of poly-A sites, can be found here.TreeLD 1.0TreeLD is a software tool for mapping complex trait loci, developed by Zollner and Pritchard (2005). TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. Download TreeLD 1.0
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