Pol tree versus LTR tree. (Left) Neighbour-joining tree based on a concatenated alignment of RT- RNAse H- and IN- sequences coming from 47 LTR retrotransposons. (Right) Two neighbour-joining trees generated from Viterbi alignments of LTR HMMs trained on sets containing HMM consensuses from Table 1. The upper tree is based on 11 consensuses whereas the lower tree is based on nine. Both are congruent, but the second has better bootstrap support. ClustalW  was used with 1,000 bootstrap replicates and default parameters.