Table 2.
Parameters and results of supertree analyses
| Partition (# of trees) | Analysis | Reps | # of trees | Program score | Recovered tree (as labeled in Fig. 3) | Software |
|---|---|---|---|---|---|---|
| Molecular (15 trees) | DFIT | All trees | 1 | 1439 | d | Clann 3.0 |
| SFIT | All trees | 1 | 1439 | d | Clann 3.0 | |
| AVCON | n/a | 1 | n/a | a | Clann 3.0 | |
| QFIT | All trees | 1 | 5.54 | d | Clann 3.0 | |
| RF | 50 | 38 | 79 | b (strict), d (majority rule) | RF-Supertrees 2.0 | |
| MRF | 90 | 1 | 47 flips | c | Rainbow 0.3 | |
| MRP | 90 | 2 | 140 steps | e, f | Rainbow 0.3 | |
| Morphology (27 trees) | DFIT | All trees | 1 | 21.52 | g | Clann 3.0 |
| SFIT | All trees | 1 | 20.25 | g | Clann 3.0 | |
| AVCON | n/a | 1 | n/a | h | Clann 3.0 | |
| QFIT | All trees | 1 | 4.91 | g | Clann 3.0 | |
| RF | 50 | 51 | 103 | g (strict and majority rule) | RF-Supertrees 2.0 | |
| MRF | 90 | 1 | 41 flips | g | Rainbow 0.3 | |
| MRP | 90 | 1 | 207 steps | g | Rainbow 0.3 |
Notes: “Reps” refers to the number of random addition sequences performed by Rainbow 0.3 and the number of ratchet search iterations performed by RF-Supertrees; program scores are those reported by each of the respective software programs.
DFIT = most similar supertrees; SFIT = maximum split fit; AVCON = average consensus; QFIT = maximum quartet fit; RF = Robinson–Foulds distance; MRF = matrix representation with flipping; MRF = matrix representation with parsimony.