[i] ^aSequence evolution further analyzed for reverse transcriptase and integrase among gypsy and copia phylogenies

[ii] ^bM0 model, one rate ratio across all codon sites and all branches of phylogeny.

[iii] ^cNearly neutral model, constrains w ratio to nearly 0 and 1.

[iv] ^dPositive selection model.

[v] ^eDiscrete model of sequence evolution with four categories (k).

[vi] ^fDiscrete model of sequence evolution estimated by fitModeL for comparison to M3 + 1.

[vii] ^gDiscrete model of sequence evolution, which allows “switches” of rates along phylogeny.