Table 2.
Results of selective regime analyses. "x", "y" and "z" refer to the three elements analyzed, with "z" being the one with coding potential, "y" a very close relative and "x" a more distant relative. In all cases except Va-rec, all elements in each analysis belong to the same family. For Va-rec, elements of the two families that give rise to the element were used. In this case, the gag sequences were not analyzed, due to the fact that they are of recombinant origin. 
| Sequences | Best model | ω in each branch | ||||||
| Family | x | y | z | a | b | c | d | |
| II (gag) | AC007112a | AC006217b | AC009526a | M0 | 0.25 | 0.25 | 0.25 | 0.25 |
| II (env) | AC007112.5 | AC006217b | AC009526.4a | M0 | 0.20 | 0.20 | 0.20 | 0.20 |
| IVb (gag) | AL161503 | AC006219a | AC007209.5 | M0 | 0.21 | 0.21 | 0.21 | 0.21 |
| IVb (RT) | AL161503.2 | AC006219 | AC007209.5 | M0 | 0.19 | 0.19 | 0.19 | 0.19 |
| IVb (IN) | AL161503.2 | AC069261.5a | AC007209.5 | M0 | 0.09 | 0.09 | 0.09 | 0.09 |
| IVb (env) | AL161503.2 | AF147263.1b | AC007209.5 | M0 | 0.24 | 0.24 | 0.24 | 0.24 |
| IVc (gag) | AL138663.1b | AC069555b | AB026642.1b | M0 | 0.19 | 0.19 | 0.19 | 0.19 |
| IVc (env) | AL138663a | AC069555b | AB026642.1b | M2 | 0.23 | 0.23 | 0.23 | 0.19 |
| Va (gag) | AP002033.1 | AL161505c | X81801 | M0 | 0.38 | 0.38 | 0.38 | 0.38 |
| Va (env) | AP002033.1 | AL161505.2a | X81801.1 | M0 | 0.30 | 0.30 | 0.30 | 0.30 |
| Va-rec (env) | AB062087b (VII) | X81801 (Va) | AB073163a | M0 | 0.21 | 0.21 | 0.21 | 0.21 |
| VI (gag) | AC007197a | AB046433e | AB046426b | M0 | 0.21 | 0.21 | 0.21 | 0.21 |
| VI (env) | AC007197.5 | AB046433.1a | AB046426.1a | M0 | 0.21 | 0.21 | 0.21 | 0.21 |
| VII (gag) | AC069555a | AB046430b | AB046426a | M0 | 0.31 | 0.31 | 0.31 | 0.31 |
| VII (RT) | AC069555a | AB046430b | AB046426a | M2 | 0.46 | 0.46 | 0.46 | 0.00 |