
Scaffold Density


Method

20

50

75

100

Average


MRP(PAUP*)

16632 (1870)

19844 (1988)

21742 (2879)

24325 (2896)

20991 (3684)

MRP(TNT)

16584 (1861)

19764 (1983)

21645 (2837)

24332 (2896)

20937 (3687)

MRL(RAxML)

16347 (1868)

19700 (1996)

21594 (2850)

24288 (2898)

20848 (3738)

SuperFine+MRP(PAUP*)

16368 (1869)

19714 (1995)

21625 (2844)

24329 (2891)

20876 (3742)

SuperFine+MRP(TNT)

16366 (1870)

19718 (1998)

21630 (2845)

24326 (2892)

20878 (3742)

SuperFine+MRL(RAxML)

16389 (1872)

19749 (1996)

21648 (2859)

24336 (2894)

20897 (3741)

True Tree

16852 (1929)

20246 (2024)

22147 (2770)

24820 (2783)

21385 (3714)

 We present the average MRL scores (ML scores under the symmetric twostate model with gammadistributed rates across sites) with respect to the MRP matrix, given as log likelihood scores) for the 1000taxon supertrees. Thus, numbers with smaller magnitude represent improvements. The scaffold density is the percentage of the full taxon set that is present in the scaffold tree. The standard deviation is shown in parenthesis. All scores are rounded to the nearest integer. The lowest MRL score (in magnitude) for each scaffold density is shown in bold.