2.6 Phylogenetic analysis
The entire cap gene sequences (n=90) of the PiCV obtained in this
study were used for 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. Maximum likelihood phylogenetic trees
were constructed with the GTR+G+I model implemented in the MEGA 5.0
software, with partial deletion to handle alignment gaps, and 1000
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).