Table 4 Alignment quality results for the Build_Fam, OrthoMCL and TribeMCL algorithms
From: Databases of homologous gene families for comparative genomics
Algo. | Families | Nb. families | Mean nb. seq. | Mean nb. sp. | Mean %Gbl. | Nb. fam. %Gbl. >50% | Mean NorMD | Nb. fam. NorMD >0.5 |
|---|---|---|---|---|---|---|---|---|
BF 50/80 | Â | 213 | 10 | 5.99 | 63% | 172 (80.8%) | 0.73 | 207 (97.2%) |
BF 40/80 | Â | 190 | 10 | 5.44 | 51% | 96 (50.5%) | 0.67 | 151 (79.5%) |
BF 40/90 | Â | 179 | 10 | 6.01 | 53% | 104 (58.1%) | 0.65 | 144 (80.4%) |
Ortho 1.1 | Seq. = 10 | 270 | 10 | 5.09 | 36% | 76 (28.1%) | 0.34 | 149 (55.2%) |
Ortho 1.5 | Â | 447 | 10 | 6.02 | 38% | 136 (30.4%) | 0.44 | 246 (55.0%) |
Ortho 4.0 | Â | 450 | 10 | 6.3 | 45% | 186 (41.3%) | 0.59 | 300 (66.7%) |
Tribe E-value | Â | 290 | 10 | 5.09 | 43% | 111 (38.3%) | 0.59 | 199 (68.6%) |
Tribe HSP | Â | 373 | 10 | 5.59 | 31% | 77 (20.6%) | 0.13 | 149 (39.9%) |
BF 50/80 | Â | 35 | 25 | 16.6 | 51% | 18 (51.4%) | 0.61 | 26 (74.3%) |
BF 40/80 | Â | 37 | 25 | 16.03 | 34% | 9 (24.3%) | 0.46 | 14 (37.8%) |
BF 40/90 | Â | 45 | 25 | 17.27 | 41% | 15 (33.3%) | 0.50 | 25 (55.6%) |
Ortho 1.1 | Seq. = 25 | 49 | 25 | 15.47 | 22% | 5 (10.2%) | 0.05 | 14 (28.6%) |
Ortho 1.5 | Â | 70 | 25 | 16.96 | 27% | 8 (11.4%) | 0.33 | 31 (44.3%) |
Ortho 4.0 | Â | 51 | 25 | 18.22 | 35% | 12 (23.5%) | 0.45 | 25 (49.0%) |
Tribe E-value | Â | 38 | 25 | 13.683 | 27% | 4 (10.5%) | 0.38 | 11 (28.9%) |
Tribe HSP | Â | 55 | 25 | 14.75 | 23% | 5 (9.1%) | 0.13 | 12 (21.8%) |
BF 50/80 | Â | 7 | 50 | 23.29 | 35% | 2 (28.6%) | 0.49 | 2 (28.6%) |
BF 40/80 | Â | 9 | 50 | 29.33 | 28% | 0 (0.0%) | 0.43 | 5 (55.6%) |
BF 40/90 | Â | 15 | 50 | 25.8 | 22% | 1 (6.7%) | 0.39 | 8 (53.3%) |
Ortho 1.1 | Seq. = 50 | 23 | 50 | 29.91 | 11% | 1 (4.3%) | -0.30 | 4 (17.4%) |
Ortho 1.5 | Â | 18 | 50 | 28.28 | 17% | 1 (5.6%) | 0.14 | 4 (22.2%) |
Ortho 4.0 | Â | 4 | 50 | 37 | 25% | 0 (0.0%) | 0.48 | 1 (25.0%) |
Tribe E-value | Â | 11 | 50 | 29.64 | 13% | 0 (0.0%) | 0.14 | 0 (0.0%) |
Tribe HSP | Â | 17 | 50 | 30.88 | 16% | 0 (0.0%) | 0.00 | 3 (17.6%) |
BF 50/80 | Â | 107 | 12.1 | 10 | 60% | 82 (76.6%) | 0.66 | 101 (94.4%) |
BF 40/80 | Â | 102 | 15.06 | 10 | 44% | 46 (45.1%) | 0.53 | 63 (61.8%) |
BF 40/90 | Â | 113 | 13.65 | 10 | 48% | 51 (45.1%) | 0.59 | 80 (70.8%) |
Ortho 1.1 | Sp. = 10 | 121 | 14.58 | 10 | 34% | 34 (28.1%) | 0.22 | 59 (48.8%) |
Ortho 1.5 | Â | 224 | 12.3 | 10 | 40% | 73 (32.6%) | 0.43 | 119 (53.1%) |
Ortho 4.0 | Â | 221 | 11.59 | 10 | 46% | 100 (45.2%) | 0.43 | 142 (64.3%) |
Tribe E-value | Â | 128 | 14.52 | 10 | 47% | 56 (43.8%) | 0.53 | 85 (66.4%) |
Tribe HSP | Â | 172 | 15.37 | 10 | 33% | 45 (26.2%) | 0.31 | 74 (43.0%) |
BF 50/80 | Â | 32 | 30.91 | 25 | 40% | 8 (25.0%) | 0.51 | 19 (59.4%) |
BF 40/80 | Â | 23 | 42.13 | 25 | 28% | 7 (30.4%) | 0.34 | 8 (34.8%) |
BF 40/90 | Â | 31 | 41.74 | 25 | 37% | 11 (35.5%) | 0.39 | 13 (41.9%) |
Ortho 1.1 | Sp. = 25 | 36 | 51 | 25 | 16% | 2 (5.6%) | 0.14 | 13 (36.1%) |
Ortho 1.5 | Â | 33 | 37.64 | 25 | 28% | 5 (15.2%) | 0.43 | 18 (54.5%) |
Ortho 4.0 | Â | 30 | 27.97 | 25 | 35% | 7 (23.3%) | 0.52 | 20 (66.7%) |
Tribe E-value | Â | 26 | 45.19 | 25 | 22% | 1 (3.8%) | 0.30 | 10 (38.5%) |
Tribe HSP | Â | 42 | 46.29 | 25 | 18% | 2 4.8%) | 0.24 | 11 (26.2%) |
BF 50/80 | Â | 13 | 61.38 | 50 | 30% | 1 (7.7%) | 0.54 | 8 (61.5%) |
BF 40/80 | Â | 34 | 181.15 | 50 | 23% | 4 (11.8%) | 0.16 | 15 (44.1%) |
BF 40/90 | Â | 23 | 206.3 | 50 | 26% | 4 (17.4%) | 0.16 | 10 (43.5%) |
Ortho 1.1 | Sp. = 50 | 55 | 70.35 | 50 | 20% | 2 (3.6%) | 0.27 | 18 (32.7%) |
Ortho 1.5 | Â | 27 | 57.04 | 50 | 27% | 2 (7.4%) | 0.50 | 14 (51.9%) |
Ortho 4.0 | Â | 5 | 53.4 | 50 | 32% | 0 (0.0%) | 0.51 | 3 (60.0%) |
Tribe E-value | Â | 19 | 87.42 | 50 | 19% | 2 (10.5%) | 0.21 | 5 (26.3%) |
Tribe HSP | Â | 30 | 87.67 | 50 | 18% | 1 (3.3%) | 0.16 | 6 (20.0%) |