Table 2

PTM vs PAUP*

Dataset

RDPII

ZILLA

U

ARB

PROTO

Taxa

218

500

6722

8780

25057


PTM


Score

33515

16218

92195

162438

810231

Time

1:18:29

2:32:03

10:39:56

24:47:00

23:49:40


PAUP*


Score

33565

16221

93106

162906

Difference

+50

+3

+911

+468

Time

0:01:28

15:42:19

20:10:42

29:13:33


TNT


Score

42166

16219

201259

170356

Difference

+8651

+1

+109064

+7918

Time

0:00:48

0:00:07

1:31:54

1:47:45


A comparison of search results between PTM and PAUP*, TNT, and DCM on several datasets. Note that in every case PTM followed by PSSS found a more parsimonious tree than PAUP* using stepwise maximum parsimony followed by TBR. In all but the smallest case, where the overhead of PTM is more difficult to overcome, this tree was found in less time. TNT finishes much faster than PTM, but finds less parsimonious trees. DCM experienced errors in processing many of the data sets and reported no score in these cases. However, the result from the successful run was inferior. Only the PTM method was able to process the largest data set of protobacteria, containing more that 25 thousand taxa.

Sundberg et al. BMC Bioinformatics 2012 13(Suppl 13):S8   doi:10.1186/1471-2105-13-S13-S8

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