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Table 2 PTM vs PAUP*

From: Phylogenetic search through partial tree mixing

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  
  1. 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.