Skip to main content

Table 3 Branch-lengths-from-reconstruction versus Tree-branch-length

From: Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

  Branch-lengths-from-reconstruction* Tree-branch-length  
   0 .0001 – .006 .0061 – .020 .0201 – .040 .0401 – .070 .0701 – .130 .1301 – .220 .2201 – .400 .4001 – 1.00 ≥ 1.001  
AF             
  0 5,891 1,292 6 4 0 0 0 0 0 3 7,196
  .0001 – .006 412 16,365 2,268 129 66 29 1 1 0 10 19,281
  .0061 – .020 130 1,576 11,110 1,829 100 93 47 1 2 12 14,900
  .0201 – .040 99 410 2,406 7,070 2,456 146 80 31 1 1 12,700
  .0401 – .070 145 274 1,591 2,795 7,045 3,475 125 66 5 5 15,526
  .0701 – .130 191 221 1,555 3,717 4,645 11,268 5,841 305 33 1 27,777
  .1301 – .220 169 89 474 1,673 3,396 5,753 10,051 10,022 583 4 32,214
  .2201 – .400 100 28 88 237 666 1,866 2,848 8,811 14,136 626 29,406
  .4001 – 1.00 10 1 2 3 8 48 63 178 2,492 3,507 6,312
BF             
  0 7,131 7,791 1,260 295 137 103 51 23 8 7 16,806
  .0001 – .006 11 11,570 4,748 1,282 575 275 90 28 15 13 18,607
  .0061 – .020 0 883 12,873 9,119 4,506 2,641 883 232 51 19 31,207
  .0201 – .040 0 10 606 6,487 8,980 5,554 2,046 779 175 13 24,650
  .0401 – .070 0 1 12 269 4,067 10,172 4,592 1,770 559 60 21,502
  .0701 – .130 1 0 0 5 115 3,887 10,244 8,278 2,757 252 25,539
  .1301 – .220 0 0 0 0 2 46 1,142 7,954 8,907 1,043 19,094
  .2201 – .400 4 0 0 0 0 0 7 350 4,737 2,175 7,273
  .4001 – 1.00 0 1 1 0 0 0 1 1 43 587 634
BC             
  0 7,142 17,555 2,581 405 173 128 71 30 10 13 28,108
  .0001 – .006 0 0 0 0 0 0 0 0 0 0 0
  .0061 – .020 0 2,683 15,870 7,557 1,317 340 122 59 21 13 27,982
  .0201 – .040 0 16 988 8,382 7,874 1,731 277 77 17 5 19,367
  .0401 – .070 0 1 60 1,074 8,310 9,621 1,240 217 46 6 20,575
  .0701 – .130 0 0 0 38 698 10,587 11,484 2,207 264 13 25,291
  .1301 – .220 0 0 0 1 10 270 5,813 13,177 2,598 36 21,905
  .2201 – .400 5 0 0 0 0 1 48 3,646 13,213 1,120 18,033
  .4001 – 1.00 0 1 1 0 0 0 1 2 1,083 2,963 4,051
  1. *Replacements per site from all fractional (AF), best fractional (BF), and best count (BC) tools.