Table 1.
Overview of reconstruction methods and corresponding abbreviations
| Abbreviation | Description | Reference | |
|---|---|---|---|
| Late-level combination: | |||
| Consensus | Majority-rule consensus | [83] | |
| MRP_BR | Matrix representation with parsimony and Baum/Ragan coding | [18,19] | |
| MRP_PU | Matrix representation with parsimony and Purvis coding | [43] | |
| MRP_I | Matrix representation with irreversible parsimony and Baum/Ragan coding | [46] | |
| MRF_BR | Matrix representation with flipping and Baum/Ragan coding | [47,48] | |
| MRF_PU | Matrix representation with flipping and Purvis coding | - | |
| MRC | Matrix representation with compatibility and Baum/Ragan coding | [50,51] | |
| MinCut | Minimal cut | [54] | |
| ModMinCut | Modified minimal cut | [55] | |
| MaxCut | Maximal cut | [57] | |
| QILI | Quartet inference and local inconsistency | [58] | |
| Medium-level combination: | |||
| SuperQP | Super quartet puzzling | [4] | |
| AvCon | Average consensus | [14,63] | |
| SDM | Super distance matrix | [15] | |
| Early-level combination: | |||
| SA | Superalignment | e.g. [11] | |