2.6 Phylogenetic analysis
The entire cap gene sequences of PiCV obtained in this study were
used for a phylogenetic analysis. All available PiCV sequence data from
different geographical locations within China (n=54) and the rest of the
world (n=72) were retrieved from the NCBI nucleotide database as
reference sequences (Table S1). Maximum likelihood phylogenetic trees
were constructed with the GTR+G+I model by using the MEGA 5.0 software,
with partial deletion to handle alignment gaps and 1,000 bootstrap
iterations. The phylogenetic tree was annotated with the Interactive
Tree Of Life (iTOL) software (http://itol.embl.de/), an online tool for
the display and annotation of phylogenetic trees (Letunic et al., 2006).