| cluster_id | description | aln_length | evolutionary_model | ML | avg_bootstrap_support | link |
| 113 | ABC transporters | 260 | RtREV+G+F | -4262.951909 | 66.800 | tree |
| 57 | ABC transporters | 479 | WAG+G+F | -12917.655451 | 85.063 | tree |
| 111 | ABC transporters | 282 | CpREV+G+F | -3274.058037 | 88.750 | tree |
| 9 | ABC transporters | 273 | WAG+G | -9304.40002 | 81.444 | tree |
| 112 | ABC transporters | 242 | CpREV+G+F | -5184.777746 | 68.273 | tree |
| 110 | ABC transporters | 381 | WAG+G+F | -7048.835609 | 86.727 | tree |
| 29_ABDI | ABC transporters (sub-families ABDI) | 341 | WAG+G+F | -77167.940733 | 61.218 | tree |
| 29_C | ABC transporters (sub-family C) | 823 | RtREV+G+F | -51925.265697 | 83.463 | tree |
| 29_F | ABC transporters (sub-family F) | 521 | RtREV+G+F | -93234.953876 | 80.954 | tree |
| 29_G | ABC transporters (sub-family G) | 575 | WAG+G+F | -85352.597963 | 82.025 | tree |
| 89 | Auxin - ABP | 159 | RtREV+G | -1130.980613 | 82.000 | tree |
| 85 | Auxin - amidohydrolase | 385 | WAG+G | -33117.169383 | 69.675 | tree |
| 33_B | Auxin - ARF | 393 | JTT+G | -40276.831227 | 78.378 | tree |
| 71 | Auxin - GH3 | 569 | JTT+G | -27662.105062 | 84.633 | tree |
| 33_A | Auxin - IAA | 171 | JTT+G | -15248.9459 | 67.414 | tree |
| 41 | Auxin - LAX | 467 | WAG+G+F | -9501.577355 | 83.938 | tree |
| 88 | Auxin - NIT | 317 | WAG+G | -6210.82061 | 62.286 | tree |
| 77 | Auxin - PIN | 473 | JTT+G | -15927.591097 | 84.556 | tree |
| 73_7 | Auxin - PINOID | 454 | JTT+G+F | -22826.072741 | 87.132 | tree |
| 45 | Auxin - TIR | 566 | JTT+G+F | -21159.569962 | 98.375 | tree |
| 25 | Auxin - YUCCA | 390 | WAG+G+F | -22200.025837 | 62.923 | tree |
| 132 | B3 transcription factors | 160 | JTT+G | -6682.391645 | 60.635 | tree |
| 12_2 | Centrin | 167 | JTT+G | -3485.328219 | 48.579 | tree |
| 28_7 | CHD7 | 969 | RtREV+G+F | -32076.574627 | 85.278 | tree |
| 19 | circadian clock/photoperiodism - CDF | 207 | JTT+G+F | -25504.065407 | 51.893 | tree |
| 74 | circadian clock/photoperiodism - FT | 171 | WAG+G | -12766.128597 | 68.617 | tree |
| 30 | circadian clock/photoperiodism - LHY/CCA1 | 202 | JTT+G | -16085.083705 | 53.587 | tree |
| 69 | circadian clock/photoperiodism - TOC1/PRR/CO/COL | 132 | JTT+G | -30060.554747 | 58.804 | tree |
| 59 | CPX | 299 | WAG+G | -15312.943224 | 82.800 | tree |
| 92 | Dynein | 3946 | RtREV+G+F | -87027.592992 | 92.000 | tree |
| 91 | Dynein | 3186 | RtREV+G+F | -345065.913867 | 90.857 | tree |
| 24 | HSP70 | 617 | RtREV+G+F | -45752.838989 | 70.024 | tree |
| 58_A | LHCP | 212 | RtREV+G+F | -23906.054532 | 68.582 | tree |
| 58_B | LHCP-like photoprotective proteins | 105 | WAG+G+F | -10935.591318 | 58.583 | tree |
| 28_2 | RAD54B | 695 | RtREV+G+F | -16136.670858 | 61.364 | tree |
| 93 | Tubulin | 441 | RtREV+G+F | -8856.910726 | 66.222 | tree |
| 94 | Tubulin | 451 | RtREV+G+F | -8401.254011 | 71.571 | tree |
| 76 | UROD | 346 | WAG+G | -18781.897152 | 77.357 | tree |
| 23 | WRKY | 172 | JTT+G | -10808.18093 | 40.794 | tree |
Listed here are all trees that are explicitly referred to in the manuscript. Some of them already have gene family annotation for some of the nodes.
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