MAFFTa was used to align the L1 nucleotide sequences of all PV types currently in PaVE. A maximum likelihood tree was constructed using PhyMLb implementing a gamma model allowing for among-site rate variation and variable substitution rates [GTR+I+G; model selected using jModeltestc]. The resulting tree is being displayed using phylotree.jsd.
a Katoh and Standley. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol.
b Guindon et al., 2010. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0.
c Darriba D et al., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods.
d phylotree.js (0.1.9): http://phylotree.hyphy.org/documentation/