Analyses of the sequences were performed using Uparse software (Uparse v7.0.1001) (Edgar 2013).
The sequences were performed using the BLAST program in the GenBank database.
Multiple sequence alignments of amino acid sequences were performed using ClustalX (version 2.0.9) (Thompson et al. [1997]).
Pairwise local and global alignments of protein sequences were performed using programs of the Emboss package.
Alignments of nucleotide and amino acid sequences were performed using CLUSTALW version 1.83 [35].
Predictions of signal sequences were performed using SignalP 3.0 (http://www.cbs.dtu.dk/services/SignalP/).dtu.dk/services/SignalP/
Phylogenetic analyses based on the partial capsid/pre-membrane and full envelope (E) sequences were performed using Clustalx 1.8 software.
Comparisons of 454 assemblies to available reference sequences were performed using MUMmer v3.20 [42] run with default options.
Alignments among DANGER genomic sequences were performed using the BLASTZ [52] tool as implemented in the zPicture web tool (http://zpicture.dcode.org) [53].
Alignments of multiple protein sequences were performed using MUSCLE [ 55].
Multiple alignments of the identified grape CDPK amino acid sequences were performed using ClustalX.
