Amino acid alignment derived from retroviral reverse transcriptase proteins, based on that described by Xiong and Eickbush (45). Sequences identified in this study are indicated in bold type. The underlined regions of the alignment were used in subsequent phylogenetic analysis. Asterisks represent in-frame stop codons, and missing data (due to frameshifts or deletions) are indicated by question marks. Three isolates, RV-brook trout, RV-brown trout, and RV-tiger salamanderI, contained large deletions and are not shown.