The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for example, to speed up work in two distant but related fields: analysis of DNA markers and preparation of natural history manuals. Both of these tasks require a significant amount of monotonous work, which could be automated with software. I developed "Ripeline and "Rmanual," two highly customizable R-based applications, designed with a goal of simplicity, reproducibility, and effectiveness. Ripeline is a pipeline that allows for a continuously updated analysis of multiple DNA markers. Rmanual is a "living book" which allows the creation and continuous update of manuals and checklists. Comparing with more traditional ways of DNA marker analysis and manual preparation, Ripeline and Rmanual allow for a significant reduction of time, which is usually spent doing repetitive tasks. They also provide tools which can be used in a broad spectrum of further applications.