Phylogenetic search through partial tree mixing

BMC Bioinformatics

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.

ISSN: 1471-2105