The phylogenomic annotation system PhyloGena was extended by a database back-end. Thereforeit was necessary to adapt the data-model of the software and to develop a database scheme.An interactive batch-mode was added to the program. Now it is possible to handle even verylarge datasets and to run many processes of PhyloGena in parallel on the same database. Furthermore,a component was developed which provides an automatic taxonomical classification of theinput sequences. Many new developed filters can be used to search the database for relevant results.This systems produces many phylogenetic trees. Additionally, the program PhyloSort wasseamlessly integrated to PhyloGena by an interface and a customized graphical user interface, tobe able to search for monophyletic clades.In this thesis, the theoretical backgrounds of phylogenetic analyses as well as their uses are introducedfirst. The used components and the new features of this software are presented from theusers and the developers point of view. Finally, the results of a test run are discussed, to demonstratethe capability of these new developments. Therefore 5000 sequences were analysedagainst different sequence databases. The results were compared to those of the programMEGAN, a popular program for analysis of meta-genomic datasets.