Current bioinformatics analyses for biodiversity from molecular sequence data are discussed on the background of next generation high throughput sequencing technologies. In particular, for creating time series of community composition data from amplicon sequencing approaches, different methods and their implications are compared: OTU-clustering vs. phylotyping, tree-based taxonomic assignment vs. assignment based on only-sequence characteristics. Software and hardware requirements as well as aspects of sustainable bioinformatics support are discussed. As a concrete example of analyses support, details of the AWI pipeline QZIP are shown.