In this paper, we present a practical experiment of building a service-oriented system upon current web services technologies and bioinformatics middleware. The system allows scientists to extract data from heterogeneous data sources and generate phylogenetic comparisons automatically. This can be difficult to accomplish using manual search tools since sequence data is rapidly accumulating. A web-based environment enables scientists to more effectively define a task, perform the task at a desired time, monitor the execution status, and view the results. The first prototype of this system is being evaluated on a phylogenetic research application, Mother of Green (MoG). Our evaluation demonstrates that a service-oriented architecture can accelerate scientific research, increase research productivity, and provide a new approach to doing science. We also discuss issues in design and implementation of the system and identify our future research directions to enhance the system.