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microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets
TLDR
A new software tool, specifically designed to facilitate the analysis of large microsatellite data sets, and an improved method to deal with inbred samples (such as Drosophila isofemale lines).
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PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
TLDR
PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data, implements a range of commonly used measures of differentiation that can be applied on different scales (windows, genes, exons, SNPs).
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PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals
TLDR
PoPoolation calculates estimates of θ Watterson, θ π, and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species.
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SciRoKo: a new tool for whole genome microsatellite search and investigation
TLDR
SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences using an extremely fast search algorithm with a built-in summary statistic tool, which makes SciRoKo an excellent tool for full genome analysis.
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Evolutionary dynamics of microsatellite DNA
TLDR
Both generally agreed and controversial results about the mutational dynamics of microsatellite DNA are reviewed.
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The evolution of molecular markers — just a matter of fashion?
In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years…
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A microsatellite-based multilocus screen for the identification of local selective sweeps.
TLDR
A new multilocus test statistic, ln RV, is introduced, which is based on the ratio of observed variances in repeat number at a set of micros Satellite loci in two groups of populations, and captures demographic history of the populations as well as variation in microsatellite mutation among loci.
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Comparative evolutionary analysis of rDNA ITS regions in Drosophila.
TLDR
The internal transcribed spacer of the ribosomal DNA is generally considered to be under low functional constraint, and it is therefore often treated as a typical nonfunctional spacer sequence, but a statistical test suggests that more than half of the spacer is apparently free to diverge and evolves with a rate that is close to the neutral rate of sequence evolution in Drosophila.
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Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
TLDR
This Review demonstrates the breadth of questions that are being addressed by Pool-seq but also discusses its limitations and provides guidelines for users.
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A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster.
TLDR
A "hitchhiking mapping" study in D. melanogaster, which searches for genomic regions with reduced variability to identify selective sweeps associated with the "out of Africa" habitat expansion, finds that some of these captured most, but not all aspects of the data.
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