A comparative evaluation of sequence classification programs

BMC Bioinformatics

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)
CARMA^1,2	290880	77340	74950	360107	200819
MEGAN^1,2	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.

ISSN: 1471-2105