In summary, we provide a sequence analysis and structural modelling of the neuraminidase from the 2009 H1N1 swine flu outbreak. Besides mapping of phylogenetic relationships to other strains, we find that the sequence variation in the new strain does not seem to affect the drug binding site but may very well alter common epitopes. To allow quick analysis of future mutations that could produce drug or vaccine-resistant strains, we provide a tool for 3D visualization of the neuraminidase structure models with mapping of drug and antibody recognition sites on the supplementary webpage http://men del.bii.a-star.edu.sg/SEQUENCES/H1N1/.