Table 1

PTM vs stepwise maximum parsimony

Dataset

RDPII

ZILLA

U

ARB

Taxa

218

500

6722

8780


PTM


Score

33534

16234

92195

162440

Time

00:00:52

00:01:23

09:30:48

21:35:32


PAUP*


Score

33934

16414

95217

165289

Difference

+400

+180

+3022

+2849

Time

<00:00:01

<00:00:0l

00:01:21

00:03:36


PAUP* (multiple trees)

Score

33855

16386

94922

165149

Difference

+321

+152

+2727

+2709

Time

00:00:58

00:01:40

06:30:44

12:18:10


A comparison of search results between PTM and stepwise maximum parsimony on several datasets. Note that in every case PTM found more parsimonious trees, but in much more time. When stepwise maximum parsimony was used to find multiple starting trees (300), PTM still found more parsimonious trees.

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

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