Phylogenetic search through partial tree mixing

BMC Bioinformatics

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.

ISSN: 1471-2105