SciRoKo enables to investigate microsatellite abundance in entire genomes. For example, the rice genome may be scanned in 55 sec. An integrated statistics module makes SciRoKo a powerful tool for comparative genomics.
A pipeline for analyzing pooled next generation sequencing data of single populations. Currently PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D using a sliding window approach.
PoPoolation2 allows to compare allele frequencies for SNPs between two or more pooled populations (Pool-Seq) and to identify significant differences. It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.
A pipeline for identifying transposable elements in pooled populations; Replaced by PoPoolationTE2
PoPoolationTE2 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 facilitates an unbiased comparison of TE abundance between samples, where samples could be pooled populations, tissues or sequenced individuals.
A tool for an unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may be used to obtain an biological interpretation of the results of PoPoolation and PoPoolation2.
A tool for simulating genotypes and phenotypes in experimentally evolving populations.
MimicrEE is a forward simulation tool of standing genetic variation, thus no 'de novo' mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs.
PanGEA allows to map EST's to genes or genomes using an algorithm especially adapted to the 454 sequencing technologies (homopolymer length polymorphism). The mapping results may be displayed as a gene-expression-profile or used for SNP identification.