Table 3.
Recombination events detected by jpHMM and RPD4 and phylogenetic analysis of the studied samples.
| jpHMM |
|||||||
|---|---|---|---|---|---|---|---|
| Sample (MP)a | Event | Subtype | Start | End | ELW | UQ | # CRs (taxa) |
| 79 (F1) | 1∗∗ | B | 2466 | 3700 | B | 0.067 | 1 (44_BF) |
| 93(F1) | 1∗∗ | B | 2467 | 3701 | B | 0.068 | 1 (44_BF) |
| 678 (G) | 1∗∗ | B | 2576 | 4830 | B | 0.037 | 1 (B) |
| 703(G) | 1∗∗ | B | 2575 | 4829 | B | 0.032 | 1(B) |
| 724(G) | 1∗∗ | B | 2576 | 4830 | B | 0.027 | 1 (B) |
| 2011 (A1) | 1∗∗ | D | 2135 | 3254 | D|b | 0.115 | 5 (D) |
| 2J∗∗ | D | 6077 | 7317 | D | 0.044 | 4 (D) | |
| 3J∗∗ | D | 7602 | 8821 | D | 0.064 | 20 (D) | |
| 4J | B | 8822 | 9199 | B|D|H|A2 | 0.109 | 19 (D) | |
| 5J∗∗ | D | 9200 | 9411 | D|b | 0.072 | 12 (D) | |
| 2104 (A1) | 1∗∗ | D | 2137 | 3255 | D|b | 0.123 | 1 (19_cpx) |
| 2J∗∗ | D | 6079 | 8818 | D | 0.018 | 4 (D) | |
| 3J | B | 8820 | 9200 | B|H|D|A2 | 0.117 | 1 (03_AB) | |
| 4J∗∗ | D | 9202 | 9412 | D|b | 0.078 | 14 (D) | |
| 3011 (A1) | 1J∗∗ | G | 1628 | 2287 | G | 0.139 | 1 (13_cpx) |
| 2J | J | 2691 | 3116 | J|K | 0.252 | 2 (27|13_cpx) | |
| 3J∗ | H | 3118 | 3224 | H|a1|a2 | 0.553 | 4 (H) | |
| 4J | B | 3483 | 4147 | K|F2|F1|G | 0.270 | 1 (04_cpx) | |
| 5J∗ | G | 4149 | 4607 | G | 0.337 | 1 (27_cpx) | |
| 6J | B | 5085 | 5706 | K|J | 0.104 | 3 (URF_U, 09_cpx, URF_0209) | |
| 7∗∗ | K | 6076 | 6296 | K | 0.149 | 1 (K) | |
| 8J∗ | H | 8335 | 8558 | H | 0.301 | 1 (04_cpx) | |
| 9J∗ | J | 8560 | 8670 | J|c|k | 0.431 | 1 (URF_A1D) | |
| 10J∗ | H | 8867 | 9018 | H | 0.269 | H | |
| 3164 (A1) | 1J∗∗ | K | 6079 | 6298 | K | 0.156 | 1 (K) |
| 2J∗ | H | 8336 | 8559 | H | 0.284 | 1 (04_cpx) | |
| 3J∗ | J | 8561 | 8663 | J|c | 0.456 | 2 (45_cpx, URF_U) | |
| 4J∗ | H | 8870 | 8998 | H | 0.376 | 4 (H) | |
| 5J | B | 9000 | 9299 | H|B|F1|F2|J|K|G|D | 0.149 | 222 (HIV-1) | |
|
RDP4 | |||||||
| Sample (MP)a | Event | Subtype | Start | End | ELW | UQ | # CRs (taxa) |
| 79 (F1) | 1∗∗ | B | 2470 | 3707 | B | 0.057 | 1 (44_BF) |
| 93 (F1) | 1∗∗ | B | 2471 | 3708 | B | 0.067 | 1 (44_BF) |
| 678 (G) | 1∗∗ | B | 2592 | 4802 | B | 0.026 | 1 (51_01B) |
| 703 (G) | 1∗∗ | B | 2558 | 4803 | B | 0.028 | 1 (B) |
| 2R | U(D) | 8697 | 8860 | J|K|B|D|H|C | 0.388 | 3 (24|23|20_BG) | |
| 724 (G) | 1∗∗ | B | 2559 | 4804 | B | 0.034 | 222 (HIV-1) |
| 2R | H | 7337 | 7612 | H|G|J | 0.281 | 3 (24|23|20_BG) | |
| 2011(A1) | 1∗∗ | D | 2161 | 3069 | D|b | 0.147 | 5 (D) |
| 2R | U(F) | 3070 | 5923 | A1 | 0.013 | 1 (A3) | |
| 3R∗∗ | D | 6077 | 9384 | D | 0 | 11 (D) | |
| 2104 (A1) | 1∗∗ | D | 2135 | 3252 | D|b | 0.154 | 5 (D) |
| 2R | U(F2) | 3253 | 5924 | A1 | 0.02 | 1 (A3) | |
| 3R∗∗ | D | 6078 | 9384 | D | 0 | 17 (D) | |
| 3011 (A1) | 1R | C | 1526 | 1989 | G|C | 0.195 | 2 (32_06A1, 06_cpx) |
| 2R | U(F1) | 2169 | 3238 | H|K|J | 0.137 | 1 (27_cpx) | |
| 3R | F2 | 3449 | 5662 | K|C|J | 0.034 | 1 (27_cpx) | |
| 7∗∗ | K | 6109 | 6486 | K | 0.125 | 1 (39_BF) | |
| 4R | U(C) | 6608 | 6847 | A2|A1|H|F2 | 0.396 | 1 (URF_U) | |
| 5R | U(F2) | 8335 | 9385 | H | 0.026 | 5 (H) | |
| 3164 (A1) | 1R∗ | K | 2727 | 3031 | K | 0.307 | 1 (49_cpx) |
| 2R | F2 | 6079 | 6345 | K | 0.172 | 2 (K) | |
Events detected by jpHMM and RDP4 are named with one single number and those detected by only one method are named with a number and a letter (J = jpHMM, R = RDP4). Asterisks indicate events confirmed by ELW (best topology) and phylogenetic signal (unresolved quartets, UQ < 0.25). Alternative topologies found by ELW (less than 0.5 difference with the best topology) are shown in lowercase. The number of closest relatives (CRs) and corresponding pure subtype or RF are shown in the last column. aMajor parental; ∗Supported by ELW; ∗∗Supported by ELW + Phylogenetic signal.