PoPoolation [Link 1] is a collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals


PoPoolation2 [Link 2] allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution


PoPoolation DB [Link 3] provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.

PoPoolationDB database for three Drosophila species

Drosophila melanogaster [Link ]

Drosophila mauritiana [Link 4]

Drosophila simulans [Link 5]

PoPoolation TE2

PoPoolationTE2 [Link 6]: enables comparative population genomics of transposable elements (TE). As a major innovation PoPoolation TE2 introduces the physical pileup file which allows to homogenize the power to identify TEs and thus enables an unbiased comparison of TE abundance between samples, where samples could be pooled populations, tissues or sequenced individuals.


Gowinda [Link 7] is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies.


Allim [Link 8], Allelic imbalance meter, offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.


DistMap [Link 9]: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster.

Microsatellite Analyzer

Microsatellite Analyzer (MSA) [Link 10] Provides basic summary statistics for microsatellite data. Written by Daniel Dieringer [Link 11] converts the output of Hudson's makesample software into microsatellite data. The output could be directly analyzed by MSA. Written by Sreenivasa Rao Pidugu


CANGS1.1 [Link 12] a user-friendly utility for processing and anylyzing 454 GS-FLX data in biodiversity studies. Written by Ram Vinay Pandey


CANGSdb [Link 13] is a stand-alone web-based database tool for processing, managing and analyzing 454 sequencing data in biodiversity studies.

Microsatellite Data

Link to analysed Microsatellite Loci [Link 14]



Institute of Population Genetics
1210 Vienna, Veterinärplatz 1
Building HA, 4th floor

T +43 1 25077-4301
F +43 1 25077-4390

Link to directions [Link 15]

Link to campus map
 [Link 16]