Alignments were generated from GenBank sequences retrieved in January 2011, aligned using Muscle [17] , rechecked and improved manually in the UTR regions. Sequences were numbered from the start of the ORFs using Neudoerfl (U27495) as reference. Details on the included sequences are provided in Table S1 . ALN1 contains 41 complete nucleotide sequences of Tick-borne encephalitis virus and three out-groups selected among LGTV and OHFV. This initial alignment was scanned for recombination events and then down sampled to an alignment (ALN2) of 28 complete sequences of known collection dates (from 1937 to 2008), with the deletion of out-groups and strains with unusual sampling locations. UTRs and gap columns were deleted. ALN2 was further partitioned by individual genes resulting in alignments ALN2_C, ALN2_PrM, ALN2_E, ALN2_NS1, ALN2_NS2A, ALN2_NS2B, ALN2_NS3, ALN2_NS4A, ALN2_NS4B and ALN2_NS5. Next, we produced ALN3 from ALN2 with the deletion of the E gene and the region of NS3 identified as a possible recombinant fragment. Finally, E_161 was compiled from the 161 longest Esequences available in Genbank (1033 to 1491 nt in length) endowed with sampling dates (from 1931 to 2008).