Maximum-likelihood phylogenetic trees of representative viral transcripts containing the RdRp from the families (A) Coronaviridae, (B) Astroviridae, (C) Paramyxoviridae, (E) Rhabdoviridae, and (F) Picornaviridae, and (D) the major capsid protein from the Papillomaviridae. Bat viruses identified in this study are in bold, while known genera and subfamilies are highlighted. Branches are scaled to the number of amino acid substitutions per site. All phylogenetic trees, with the exception of that of the Coronaviridae which was manually rooted, were midpoint rooted. Nodes with ultrafast bootstrap values of >70 per cent are noted. Below each phylogenetic tree is the genomic organization that shows the closest BLASTp hit, with the polymerase or capsid region highlighted. Novel bat viral contigs have been aligned to the closest BLASTp hits and the mean pairwise identity of the alignment as well as the amino acid length of the alignment are shown.