Gegenees is a software that compares genome sequences (Draft and Completed). It was primarily developed for bacterial genomes but it is also possible to use on viruses and smaller eukaryotes. Gegenees fragments the genomes and compares all pieces against all genomes. Based on this all-against-all comparison, a phylogenetic data can be extracted. It is also possible to define a "target group" and search for genomic regions that have high specificity for the target group. This is referred to as a "genomic signature". The genomic signature regions can be used to find candidate regions for the design of primers and probes for ne highly specific diagnostic assays. There is also a built in primer/probe verification system that compares new candidate or existing primers and probes to the genomic database and to the defined target groups. Future versions will include more aspects of comparing next generation sequencing (NGS) data .