Comparisons of pol gene nucleotide and reverse transcriptase (RT) amino acid 
sequences of 47 retroviruses, 3 caulimoviruses, and 5 hepadnaviruses showed that 
approximately one-third of the gene at the 5' end is much more conserved than 
other pol regions. The most conserved regions on both the nucleotide and amino 
acid sequences were chosen for construction of phylogenetic trees. The 
maximum-parsimony and distance-matrix methods were used for analyses of aligned 
amino acid sequences; these two methods, and the compatibility method, were used 
to analyze the aligned nucleotide sequences. Essentially identical majority-rule 
consensus trees were produced by these different methods from both the pol gene 
nucleotide and RT amino acid sequences, which divided the 55 retroelements into 
six major groups. The reliability of the phylogenetic trees was probed with the 
bootstrapping of 100 replicates of the original sequence alignments. The 
grouping results were shown to be statistically significant by multiple 
comparisons with the least-significant-difference procedure.