J. Hein et J. Stovlbaek, A MAXIMUM-LIKELIHOOD APPROACH TO ANALYZING NONOVERLAPPING AND OVERLAPPING READING FRAMES, Journal of molecular evolution, 40(2), 1995, pp. 181-189
A model is presented for sequence evolution on the basis of which one
can analyze combinations of noncoding, singly coding, and multiply cod
ing regions of aligned homologous DNA sequences. It is a generalizatio
n of Kimura's (J. Mol. Evol. 16:111-120, 1980) and Li et al.'s (J. Mol
. Evol. 36:96-99, 1985) transition-transversion models with selection
on replacement substitutions. Based on a hierarchy of hypotheses, one
will be able to estimate selection factors and transition and transver
sion distances for different combinations of regions ranging from many
regions, each with their private set of parameters, to one set of par
ameters for all regions. The method is demonstrated on two aligned HIV
1 retroviruses.