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Table 3 Performance comparison between ENVirT, PHACCS and CatchAll on simulated contig spectra

From: ENVirT: inference of ecological characteristics of viruses from metagenomic data

Input parameters (expected result)

ENVirT

PHACCS

CatchAll

L 0

M 0

T 0

d 0

Evenness

f max

M

T

d

S min

M

T

d

S min

M

12500

300

exp

0.030

0.790

2.956%

300

exp

0.030

0.00x10 0

4096

exp

0.030

1.37x10 -3

2829.6 p

12500

1000

log

0.900

0.995

0.661%

1000

log

0.900

0.00x10 0

1000

log

0.900

0.00x10 0

92628.3 c

12500

5000

lgn

2.500

0.655

11.849%

5000

lgn

2.500

0.00x10 0

23563

pl

1.313

1.01x10 4

3246.1 p

12500

10000

pl

0.700

0.913

1.997%

10000

pl

0.700

0.00x10 0

10000

pl

0.700

0.00x10 0

696.3 p

50000

300

exp

0.030

0.790

2.956%

300

exp

0.030

0.00x10 0

10000

exp

0.030

4.31x10 -4

15712.6 p

50000

1000

log

0.900

0.995

0.661%

1000

log

0.900

0.00x10 0

1000

log

0.900

0.00x10 0

n/a

50000

5000

lgn

2.500

0.655

11.849%

5000

lgn

2.500

0.00x10 0

4996

lgn

2.500

1.78x10 -3

799.8 p

50000

10000

pl

0.700

0.913

1.997%

10000

pl

0.700

0.00x10 0

10000

pl

0.700

0.00x10 0

413688.9 c

125000

300

exp

0.030

0.790

2.956%

300

exp

0.030

0.00x10 0

10000

exp

0.060

1.87x10 -4

70340.9 c

125000

1000

log

0.900

0.995

0.661%

1000

log

0.900

0.00x10 0

1000

log

0.900

0.00x10 0

n/a

125000

5000

lgn

2.500

0.655

11.849%

5000

lgn

2.500

0.00x10 0

5000

lgn

2.500

0.00x10 0

2303.2 p

125000

10000

pl

0.700

0.913

1.997%

10000

pl

0.700

0.00x10 0

10000

pl

0.700

0.00x10 0

n/a

300000

300

exp

0.030

0.790

2.956%

300

exp

0.030

0.00x10 0

4096

exp

0.030

7.92x10 -5

160243.9 c

300000

1000

log

0.900

0.995

0.661%

1000

log

0.900

0.00x10 0

1000

log

0.900

0.00x10 0

n/a

300000

5000

lgn

2.500

0.655

11.849%

5000

lgn

2.500

0.00x10 0

5000

lgn

2.500

0.00x10 0

146552.7 c

300000

10000

pl

0.700

0.913

1.997%

8547

pl

0.689

3.00x10 -3

10000

pl

0.700

0.00x10 0

n/a

  1. Contig spectra were generated with parameters: R=10000, r= 100bp and o= 35bp. Both ENVirT and PHACCS were provided with the true average genome length (L0) value. pl = power-law distribution, exp = exponential distribution, log = logarithmic distribution and lgn = lognormal distribution. Smin = the value of the cost function corresponding to the estimated values of M,T and d for each method. For each spectrum, the CatchAll estimate having the minimum error compared to M0 is reported. p = best discounted parametric model produced by CatchAll. c = Chao1 non-parametric estimate. n/a denotes samples for which CatchAll failed to produce an output