Phylogenetic analysis of concatenated VP1 and Large T proteins from avian and mammalian polyomaviruses. Sequence alignments were made by using MacVector version 10.6. The GapStreeze program (Los Alamos HIV Sequence Database; http://www.hiv.lanl.gov/content/sequence/GAPSTREEZE/gap.html webcite) was used to remove columns with a gap tolerance of 0%. Phylogenetic analysis was performed by the neighbor-joining method using the JTT matrix model as implemented in MEGA version 4 . Bootstrap values (as % of 1000 re-samplings) are indicated. Bar, 0.06 amino acid residue replacements per site. The GenBank accession numbers of the viruses used are: NC_001515 (MuPyV), NC_001663 (HaPyV), HM355825 (McPyV), M30540 (LPV), NC_001442 (BoPyV), NC_009951 (SquiPyV), NC_011310 (MyoPyV), NC_007922 (CrPyV), NC_004800 (GoPyV), AB453166 (BFDPyV), NC_001669 (SV40), NC_001699 (JCV), AY614708 (SA12), NC_001538 (BKV), EF127906 (KIPyV), EF444549 (WUPyV), FN356900 (OraPyV-Bor), FN356901 (OraPyV-Sum), GU989205 (TSPyV), NC_014407 (HPyV6), NC_014407 (HPyV7), NC_013796 (CSLPyV1). Chimpanzee polyomaviruses are highlighted.
Deuzing et al. Virology Journal 2010 7:347 doi:10.1186/1743-422X-7-347