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Table 1 Performance of ENVirT in comparison to standard GA algorithm on simulated contig spectra

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

Input parameters (expected result) Estimated values by ENVirT Estimated values by GA without niching
L 0 M 0 T 0 d 0 Evenness f max L M T d S min L M T d S min
12500 300 exp 0.030 0.790 2.956% 12500 300 exp 0.030 0.00x10 0 39500 12400 exp 0.095 3.49x10 -2
12500 1000 log 0.900 0.995 0.661% 14972 838 log 0.893 6.56x10 -3 310000 100 lgn 1.063 2.59x10 1
12500 5000 lgn 2.500 0.655 11.849% 12500 5000 lgn 2.500 0.00x10 0 12500 5000 lgn 2.500 0.00x10 0
12500 10000 pl 0.700 0.913 1.997% 12500 10000 pl 0.700 0.00x10 0 29500 1400 log 1.911 6.38x10 0
50000 300 exp 0.030 0.790 2.956% 50000 300 exp 0.030 0.00x10 0 41000 100 pl 0.378 1.53x10 1
50000 1000 log 0.900 0.995 0.661% 50000 1000 log 0.900 0.00x10 0 100500 600 lgn 0.531 3.48x10 -2
50000 5000 lgn 2.500 0.655 11.849% 50000 5000 lgn 2.500 0.00x10 0 50000 5100 lgn 2.506 1.92x10 -2
50000 10000 pl 0.700 0.913 1.997% 52787 10175 pl 0.707 1.72x10 -3 41000 9800 pl 0.677 2.22x10 -2
125000 300 exp 0.030 0.790 2.956% 125000 300 exp 0.030 0.00x10 0 58500 11000 exp 0.014 2.70x10 -2
125000 1000 log 0.900 0.995 0.661% 125000 1000 log 0.900 0.00x10 0 69000 1800 log 0.943 3.94x10 -4
125000 5000 lgn 2.500 0.655 11.849% 125000 5000 lgn 2.500 0.00x10 0 125000 5000 lgn 2.500 0.00x10 0
125000 10000 pl 0.700 0.913 1.997% 116341 9824 pl 0.691 1.96x10 -4 203000 15000 lgn 1.922 9.34x10 -1
300000 300 exp 0.030 0.790 2.956% 300000 300 exp 0.030 0.00x10 0 67000 400 lgn 0.543 5.36x10 -2
300000 1000 log 0.900 0.995 0.661% 217303 1373 log 0.899 1.26x10 -7 156000 1900 log 0.931 1.93x10 -5
300000 5000 lgn 2.500 0.655 11.849% 300000 5000 lgn 2.500 0.00x10 0 310000 7400 lgn 2.635 1.09x10 -1
300000 10000 pl 0.700 0.913 1.997% 277000 9800 pl 0.690 3.00x10 -5 77000 5600 log 1.658 2.97x10 -2
  1. Contig spectra were generated with parameters: R=10000, r=100bp and o=35bp. pl = power-law distribution, exp = exponential distribution, log = logarithmic distribution and lgn = lognormal distribution. fmax= relative abundance of the dominant genotype. Smin= the value of the cost function corresponding to the estimated values of M,L,T and d. GA = Genetic Algorithm. We chose MLB=1,MUB=15000,LLB=10000,LUB=310000,dLB=0.01 and dUB=5 for both ENVirT and GA without niching. In order to apply the second niching strategy of ENVirT, we chose NL=29