Sequence data collection and alignment H5N1 influenza viruses isolated from avian and mammalian hosts in Indonesia during 2003-2007 were studied. Their genomic sequences (n = 807) were extracted from the Influenza Virus Resource [53] and the Influenza Sequence Database [54] in September 2007, and aligned using MUSCLE version 3.6 [55] . Columns with gaps were removed from the alignments, and sequences from the same virus strain (duplicated submission in the two databases) were filtered such that one copy was retained. Eight genome segment alignment datasets (PB2, PB1, PA, HA, NP, NA, MP, and NS), as well as four coding sequences (M1, M2, NS1, and NS2), were generated. Full details of our datasets can be found in Table S6 and S7.