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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).