In this recombination-based cloning pipeline, viral ORFs amplified by PCR or RT-PCR are cloned by in vitro recombination into donor vectors such as pDONR207 or pDONR223 (see Supplementary Data for detailed protocols). After transformation, a construct can be purified either from a mini-pool of bacteria colonies to keep the sequence diversity of the original template (e.g. when working with viral quasi-species) or from a single isolated colony. These two cloning strategies, referred as 1.0 and 2.0, respectively (5), are manageable using ViralORFeome interface (Figure 2 ).