Websites:

ICTV Flaviviridae Study Group (dengue virus and hepatitis C virus subtypes):

https://talk.ictvonline.org/ictv_wikis/flaviviridae/w/sg_flavi

Sequence alignments and tree files:

Figure 1.Flaviviridae: 

Tree file (newick format)

Alignment file (FASTA format)

Figure 3.Pestivirus: 

Tree file (newick format)

Alignment file - amino acid (FASTA format)

Alignment file - nucleotide (FASTA format)