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Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θ(Watterson), θ(π),(More)
SUMMARY Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (F(ST),(More)
MOTIVATION Despite increased availability of genome annotation data, a comprehensive resource for in-depth analysis of splice signal distributions and alternative splicing (AS) patterns in eukaryote genomes is still lacking. To meet this need, we have developed EuSplice--a unique splice-centric database which provides reliable splice signal and AS(More)
With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a(More)
Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing(More)
BACKGROUND Next generation sequencing (NGS) technologies have substantially increased the sequence output while the costs were dramatically reduced. In addition to the use in whole genome sequencing, the 454 GS-FLX platform is becoming a widely used tool for biodiversity surveys based on amplicon sequencing. In order to use NGS for biodiversity surveys,(More)
Due to its cost effectiveness, next-generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for characterizing variation in population samples. Because Pool-Seq provides genome-wide SNP frequency data, it is possible to use them for demographic inference and/or the identification of selective sweeps. Here, we introduce a(More)
Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user-friendly software tool, Allim, to estimate allele-specific gene expression. Because mapping bias is a major problem for reliable estimates of allele-specific gene expression using RNA-seq, Allim combines two different(More)
It is generally accepted that gene regulation serves an important role in determining the phenotype. To shed light on the evolutionary forces operating on gene regulation, previous studies mainly focused on the expression differences between species and their inter-specific hybrids. Here, we use RNA-Seq to study the intra-specific distribution of cis- and(More)
BACKGROUND The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses. With the new sequencing technologies it has become feasible to collect sequence information for multiple(More)