Table 3

Optimal parameters

Algorithm

Parameter

Optimized for accuracy

Optimized for separation


MCL

Inflation

1.8

1.8


MCODE

Depth

100

5

Node score percentage

0

0

Haircut

TRUE

TRUE

Fluff

FALSE

FALSE

Percentage for complex fluffing

0.2

0.9


RNSC

Diversification frequency

50

50

Shuffling diversification length

9

3

Tabu length

50

50

Tabu list tolerance

1

1

Number of experiments

3

3

Naive stopping tolerance

1

15

Scaled stopping tolerance

15

15


SPC

Number of nearest neighbours

15

10

Temperature

0.132

0.116


Brohée and van Helden BMC Bioinformatics 2006 7:488   doi:10.1186/1471-2105-7-488

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