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Table 1 Time to completion (in seconds) of the Cluster Picker and PhyloPart for data sets of increasing sizes

From: Automated analysis of phylogenetic clusters

Number of sequences Cluster Picker (s) PhyloPart (s)
1000 13.098 8.913
2000 36.137 44.151
3000 68.772 112.729
4000 115.618 672.085
5000 173.584 1447.047
6000 244.290 1713.749
7000 328.651 2190.336
8000 419.369 1081.785
9000 526.070 1043.838
10000 658.607 2321.955
11000 769.469 2343.197
12000 911.086 3061.134
13000 1059.509 2851.417
14000 1228.151 2078.609
15000 1383.366 2625.491
16000 1581.351 2797.329
17000 1775.639 3047.713
18000 1990.372 NA
  1. Notes: Both programs were run on a Windows desktop computer with an Intel Core i5-2400 3.10 GHz with 4 processors, reserving 1.5 G of heap space. PhyloPart did not complete on the desktop computer with n = 18,000 sequences as heap space could not be increased. Settings were left as default in the Cluster Picker and set at t = 0.05 in PhyloPart. For 10,000 sequences, program specific RAM usage was 265,000 K for PhyloPart and 100,000 K for the CP. Computational complexity approximately O(n2) for this data set (see Additional file 5).