Table 2

Performance of alignment-based programs
Program FACS 269 bp MetaPhyler 300 bp CARMA 265 bp PhyloPythia 961 bp Mean
Percentage of sequence classified
CARMA 29.0 93.6 68.7 61.3 63.2
MEGAN 48.4 88.2 90.5 62.2 72.3
MetaPhyler 0.2 80.9 0.5 0.6 20.6
MG-RAST 27.1 29.8 80.2 70.5 51.9
Sensitivity (percentage)
CARMA 26.7 93.4 68.5 59.8 62.1
MEGAN 42.5 87.9 90.3 61.0 70.4
MetaPhyler 0.1 80.7 0.5 0.5 20.5
MG-RAST 25.0 29.7 80.1 67.2 50.5
Precision (percentage)
CARMA 92.0 99.7 99.7 97.4 97.2
MEGAN 78.1 99.7 99.8 98.1 93.9
MetaPhyler 84.0 99.7 100.0 83.8 91.9
MG-RAST 92.4 99.8 99.9 95.3 96.9
CPU Runtime (minutes)
CARMA1,2 290880 77340 74950 360107 200819
MEGAN1,2 288020 72060 72010 351060 195788
MetaPhyler3 10 20 2 28 15
MG-RAST4 60 10080 20160 12960 10815
Memory Usage (Megabytes of RAM)
CARMA 100 100 100 120 105
MEGAN 1024 1024 1024 1410 1121
MetaPhyler 5734 5734 5734 5734 5734
MG-RAST5 - - - - -

Measurements of sensitivity, precision, and resource consumption on four simulated data sets.

1analysis performed on a 2.66 GHz Intel Core i7 MacBook Pro running Mac OS X 10.7.1 with 8 GB 1067 MHz DDR3 RAM.

2BLAST v2.2.18 analysis performed using ∼200 Opteron 2425 HE (2.1GHz) cores; each node has 48G RAM.

3analysis performed on an AMD Opteron 250 (2.4 GHz) Sun Fire V40z with 32 GB RAM.

4used web service; recorded value is number of minutes to receive results, not actual CPU runtime.

5used web service; memory usage was unable to be determined.

Bazinet and Cummings

Bazinet and Cummings BMC Bioinformatics 2012 13:92   doi:10.1186/1471-2105-13-92

Open Data