Supplementary Trees for Rensing et al 2007

Annotated bootstrapped RAxML ML trees (BKL) with exact parameter estimation, 4 rate categories (PROTMIX) and ProtTest-assisted model selection

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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