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Table 1 Comparison of MEC and runtimes for different schemes applied to HuRef data

From: SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming

chr # Huref
  CPLEX SDhaP HAPCUT RefHap HapTree
  MEC t(in secs) MEC t(in secs) MEC t(in secs) MEC t(in secs) MEC t(in secs)
1 16853 1.72×105 17192 190 19777 251 18739 8354 21112 8499
2 12618 1260 12713 220 14698 185 13762 3576 15720 8210
3 9296 960 9444 153 10714 257 10096 4866 11424 12183
4 9958 1140 10106 115 11567 274 10936 5399 12479 9534
5 9195 1080 9333 141 10590 196 10045 4398 11391 8972
6 8637 900 8696 105 9922 247 9318 4225 10912 8462
7 9782 1020 9954 102 11279 152 10540 7030 12196 6876
8 8480 3960 8604 90 9832 226 9352 4640 10552 9162
9 8051 780 8134 88 9290 111 8850 3898 9905 5515
10 8550 1200 8680 87 9877 209 9323 5203 10598 8782
11 7027 840 7186 92 8210 156 7744 4514 8856 7093
12 7136 720 7256 100 8240 152 7725 2669 9003 5494
13 5090 600 5142 62 5844 125 5511 3363 6285 7680
14 5086 480 5173 52 5861 72 5537 2313 6273 3533
15 8088 1.67×105 8216 71 9364 108 9031 2014 10218 4018
16 7176 1500 7231 51 8287 138 7830 1896 8769 4589
17 5739 480 5819 47 6570 86 6238 2362 7106 5626
18 4403 540 4467 56 5041 108 4814 1542 5500 3544
19 4628 480 4670 32 5335 65 5052 1132 5660 2804
20 3243 300 3316 37 3753 63 3458 1472 4068 3602
21 3360 2400 3369 31 3914 63 3752 739 4154 1692
22 3908 7.16×105 3973 32 4539 43 4384 1786 4780 1683
  1. MEC and running times for CPLEX, SDhaP, HAPCUT, RefHap and HapTree algorithms applied to HuRef data. SDhaP is more accurate than all schemes except for CPLEX (which is the only one that requires proprietary software). However, for longer blocks, the complexity of the CPLEX scheme may become very high as evident from chromosomes 1, 15 and 22.