From: Reconstruction of ancestral protein sequences and its applications
Root Seq. | Tree | Leaf Node Num. | Methods | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
 |  |  | ANCESCON | PAML | PHYLIP $ | PAUP* | ||||||
 |  |  | α ML | α AB | -α | +α | -α | +L +α | -L +α | +L -α | -L -α |  |
1em2 | pii1 | 25 | 0.45 | 0.32 | 0.35 | 0.41 | 0.37 | 0.29 | 0.27 | 0.21 | 0.29 | 0.26 |
1g9o | pii1 | 25 | 0.56 | 0.46 | 0.47 | 0.53 | 0.53 | 0.51 | 0.54 | 0.40 | 0.51 | 0.47 |
1rgg | pii1 | 25 | 0.60 | 0.42 | 0.47 | 0.60 | 0.62 | 0.47 | 0.58 | 0.32 | 0.56 | 0.47 |
1sgt | pii1 | 25 | 0.38 | 0.34 | 0.33 | 0.33 | 0.32 | 0.32 | 0.33 | 0.27 | 0.33 | 0.32 |
1zm2 | pii1 | 25 | 0.33 | 0.29 | 0.3 | 0.28 | 0.25 | 0.21 | 0.25 | 0.21 | 0.27 | 0.16 |
2a8v | pii1 | 25 | 0.62 | 0.45 | 0.42 | 0.56 | 0.55 | 0.44 | 0.46 | 0.28 | 0.50 | 0.36 |
2ctb | pii1 | 25 | 0.53 | 0.40 | 0.39 | 0.41 | 0.38 | 0.24 | 0.24 | 0.21 | 0.29 | 0.22 |
Average accuracy | 0.496 | 0.383 | 0.390 | 0.446 | 0.431 | 0.354 | 0.381 | 0.271 | 0.393 | 0.323 | ||
2ctb | gef | 27 | 0.54 | 0.37 | 0.38 | 0.35 | 0.35 | 0.29 | 0.17 | 0.24 | 0.22 | 0.22 |
2ctb | LacI | 54 | 0.66 | 0.64 | 0.57 | 0.44 | 0.37 | 0.49 | 0.35 | 0.42 | 0.33 | 0.34 |
2ctb | pdz | 39 | 0.54 | 0.41 | 0.42 | 0.44 | 0.39 | 0.22 | 0.34 | 0.18 | 0.32 | 0.22 |
2ctb | ph | 30 | 0.79 | 0.74 | 0.75 | 0.53 | 0.55 | 0.45 | 0.25 | 0.43 | 0.37 | 0.32 |
2ctb | pii1 | 25 | 0.53 | 0.40 | 0.39 | 0.41 | 0.38 | 0.24 | 0.24 | 0.21 | 0.29 | 0.22 |
2ctb | ptb | 29 | 0.58 | 0.39 | 0.43 | 0.39 | 0.38 | 0.29 | 0.23 | 0.26 | 0.24 | 0.23 |
2ctb | sh2 | 34 | 0.61 | 0.42 | 0.40 | 0.43 | 0.40 | 0.30 | 0.22 | 0.20 | 0.27 | 0.22 |
2ctb | sh3 | 43 | 0.83 | 0.82 | 0.80 | 0.62 | 0.55 | 0.69 | 0.45 | 0.66 | 0.46 | 0.54 |
2ctb | GST | 140 | 0.76 | 0.73 | 0.73 | @ | @ | # | # | 0.47 | 0.38 | 0.33 |
Average accuracy& | 0.635 | 0.524 | 0.518 | 0.451 | 0.421 | 0.371 | 0.281 | 0.325 | 0.313 | 0.289 | ||
1em2 | pdz | 39 | 0.45 | 0.35 | 0.36 | 0.44 | 0.44 | 0.29 | 0.43 | 0.23 | 0.4 | 0.24 |
1g9o | pii1 | 25 | 0.56 | 0.46 | 0.47 | 0.53 | 0.53 | 0.51 | 0.54 | 0.40 | 0.51 | 0.47 |
1rgg | sh2 | 34 | 0.64 | 0.48 | 0.46 | 0.61 | 0.61 | 0.56 | 0.59 | 0.34 | 0.6 | 0.41 |
1sgt | gef | 27 | 0.49 | 0.39 | 0.40 | 0.48 | 0.44 | 0.42 | 0.44 | 0.36 | 0.45 | 0.41 |
1zm2 | ptb | 29 | 0.66 | 0.47 | 0.48 | 0.57 | 0.57 | 0.53 | 0.51 | 0.32 | 0.52 | 0.41 |
2a8v | ph | 30 | 0.81 | 0.78 | 0.81 | 0.71 | 0.74 | 0.60 | 0.61 | 0.50 | 0.65 | 0.50 |
2ctb | LacI | 54 | 0.66 | 0.64 | 0.57 | 0.44 | 0.37 | 0.49 | 0.35 | 0.42 | 0.33 | 0.34 |
Average accuracy | 0.610 | 0.510 | 0.507 | 0.540 | 0.529 | 0.486 | 0.496 | 0.367 | 0.494 | 0.397 | ||
ProbabilityΔ |  | 0.0026 | 0.0023 | 0.0248 | 0.0328 | 0.0007 | 0.0168 | 0.0001 | 0.0143 | 0.0005 |