PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).
CONCLUSIONS
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), Fisher's exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer.


METHODS
PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/popoolation2/


BACKGROUND
christian.schloetterer@vetmeduni.ac.at


BACKGROUND
Manual: http://code.google.com/p/popoolation2/wiki/Manual Test data and tutorial: http://code.google.com/p/popoolation2/wiki/Tutorial Validation: http://code.google.com/p/popoolation2/wiki/Validation.
Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria.
Robert
R
Kofler
Ram Vinay
RV
Pandey
Christian
C
Schlötterer
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D005828:Genetics, Population / Q000379:methods*; D023281:Genomics; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software