Table 1 Average adjacency reconstruction, in terms of true positives (TP) and false positives (FP) for all tested algorithms, for all datasets grouped by tree diameter
From: Fast ancestral gene order reconstruction of genomes with unequal gene content
Diameter (D) | 0.5 n | 1.0 n | 1.5 n | 2.0 n | 2.5 n | |||||
|---|---|---|---|---|---|---|---|---|---|---|
Adjacency results (%) | TP | FP | TP | FP | TP | FP | TP | FP | TP | FP |
Unitary Indels | ||||||||||
RINGO – Sim. branch lengths | 99.8 | 0.2 | 99.1 | 0.7 | 94.0 | 3.1 | 87.9 | 4.3 | 81.8 | 5.5 |
RINGO – Est. branch lengths with ME | 99.8 | 0.2 | 99.0 | 0.7 | 93.7 | 3.0 | 87.7 | 4.1 | 80.6 | 5.6 |
RINGO – Est. branch lengths with LS | 99.8 | 0.2 | 99.0 | 0.7 | 93.4 | 3.0 | 86.7 | 4.1 | 80.7 | 5.4 |
RINGO – DeClone weights, k T=0.1 | 99.6 | 0.6 | 98.1 | 2.0 | 92.1 | 7.8 | 86.9 | 8.7 | 80.7 | 11.0 |
RINGO – DeClone weights, k T=0.4 | 99.6 | 0.6 | 98.1 | 1.9 | 92.5 | 9.1 | 88.4 | 9.9 | 82.7 | 16.8 |
RINGO – DeClone weights, k T=0.8 | 99.2 | 1.2 | 97.5 | 2.9 | 91.8 | 9.9 | 88.0 | 10.5 | 82.5 | 17.1 |
MLGO | 99.6 | 0.3 | 98.6 | 1.3 | 94.6 | 5.0 | 91.8 | 7.8 | 85.6 | 13.8 |
MGRA | 99.9 | 0.0 | 99.3 | 0.5 | 95.1 | 3.5 | 85.8 | 12.8 | 70.4 | 26.7 |
Indel length ∈[1,5] | ||||||||||
RINGO – Sim. branch lengths | 99.4 | 0.3 | 96.7 | 1.4 | 92.0 | 2.6 | 73.8 | 6.2 | 81.0 | 4.9 |
RINGO – Est. branch lengths with ME | 99.4 | 0.3 | 96.6 | 1.4 | 91.6 | 2.6 | 71.8 | 5.8 | 79.5 | 4.3 |
RINGO – Est. branch lenghts with LS | 99.4 | 0.2 | 96.7 | 1.4 | 91.4 | 2.6 | 70.2 | 5.1 | 77.0 | 3.8 |
RINGO – DeClone weights, k T=0.1 | 99.3 | 0.7 | 95.4 | 5.7 | 90.6 | 10.4 | 72.0 | 14.1 | 79.3 | 13.4 |
RINGO – DeClone weights, k T=0.4 | 99.3 | 0.7 | 95.7 | 5.7 | 91.3 | 11.0 | 75.2 | 19.9 | 82.1 | 16.9 |
RINGO – DeClone weights, k T=0.8 | 99.1 | 1.1 | 95.1 | 6.8 | 90.7 | 12.3 | 74.9 | 20.3 | 81.9 | 17.4 |
MLGO | 98.9 | 0.7 | 95.9 | 3.7 | 90.6 | 7.0 | 75.0 | 15.9 | 81.7 | 13.8 |
MGRA | 99.3 | 0.3 | 99.7 | 0.3 | 94.8 | 3.8 | 65.5 | 34.5 | 57.4 | 42.4 |