Table 2

Comparison of BPs among trees 1 to 3 analyzed with concatenate and separate models
Model
 #c
 Ln L
 #p
 #s
 #s/#p
 AIC
 AICc
 Tree 1
 Tree 2
 Tree 3
Nucleotide (GTR + Γ8)
 1
 -4,076,316.3
 26
 1,011,870
 38,918.1
 8,152,684.6
 8,152,684.6
 0.0
 0.0
 100.0

5
 -4,059,904.9
 130
 1,011,870
 7,783.6
 8,120,069.8
 8,120,069.8
 0.0
 0.0
 100.0

10
 -4,058,547.6
 260
 1,011,870
 3,891.8
 8,117,615.2
 8,117,615.3
 0.0
 0.0
 100.0

56
 -4,055,469.5
 1,456
 1,011,870
 695.0
 8,113,851.0
 8,113,855.2
 0.1
 0.0
 99.9

100
 -4,053,634.1
 2,600
 1,011,870
 389.2
 8,112,468.2
 8,112,481.6
 0.1
 0.0
 99.9

200
 -4,049,237.9
 5,200
 1,011,870
 194.6
 8,108,875.8
 8,108,929.5
 0.2
 0.0
 99.8

558
 -4,035,535.0
 14,508
 1,011,870
 69.7
 8,100,086.0
 8,100,508.1
 1.7
 0.0
 98.3

930
 -4,022,303.0
 24,180
 1,011,870
 41.8
 8,092,966.0
 8,094,150.0
 3.6
 0.0
 96.4

1,395
 -4,006,623.4
 36,270
 1,011,870
 27.9
 8,085,786.8
 8,088,483.7
 25.0
 0.7
 74.3

2,789
 -3,963,489.9
 72,514
 1,011,870
 14.0
 8,072,007.8
 8,083,203.5
 86.2
 4.1
 9.7
Codon (+ Γ4)
 1
 -3,828,351.7
 81
 337,290
 4,164.1
 7,656,865.4
 7,656,865.4
 88.1
 11.3
 0.6

5
 -3,810,589.3
 405
 337,290
 832.8
 7,621,988.6
 7,621,989.6
 94.3
 5.1
 0.7

10
 -3,808,198.7
 810
 337,290
 416.4
 7,618,017.4
 7,618,021.3
 93.3
 5.9
 0.8

56
 -3,802,941.9
 4,536
 337,290
 74.4
 7,614,955.8
 7,615,079.5
 93.0
 5.2
 1.7

100
 -3,799,324.6
 8,100
 337,290
 41.6
 7,614,849.2
 7,615,247.9
 94.0
 4.9
 1.1

200
 -3,791,928.7
 16,200
 337,290
 20.8
 7,616,257.4
 7,617,892.2
 91.0
 8.1
 1.0

558
 -3,766,336.0
 45,198
 337,290
 7.5
 7,623,068.0
 7,637,056.1
 96.7
 2.9
 0.3

930
 -3,741,173.9
 75,330
 337,290
 4.5
 7,633,007.8
 7,676,332.8
 98.0
 1.7
 0.3

1,395
 -3,712,084.5
 112,995
 337,290
 3.0
 7,650,159.0
 7,764,009.4
 96.2
 3.8
 0.0

2,789
 -3,621,322.1
 225,909
 337,290
 1.5
 7,694,462.2
 8,610,876.3
 89.6
 10.4
 0.0
Amino acid (JTT-F + Γ8)
 1
 -1,905,933.9
 37
 337,290
 9,115.9
 3,811,941.8
 3,811,941.8
 51.6
 0.2
 48.2

5
 -1,879,320.4
 185
 337,290
 1,823.2
 3,759,010.8
 3,759,011.0
 63.4
 0.2
 36.5

10
 -1,877,405.7
 370
 337,290
 911.6
 3,755,551.4
 3,755,552.2
 63.9
 0.3
 35.9

56
 -1,875,094.5
 2,072
 337,290
 162.8
 3,754,333.0
 3,754,358.6
 56.6
 0.1
 43.2

100
 -1,873,607.4
 3,700
 337,290
 91.2
 3,754,614.8
 3,754,696.9
 58.7
 0.5
 40.9

200
 -1,870,213.5
 7,400
 337,290
 45.6
 3,755,227.0
 3,755,559.0
 59.8
 0.2
 40.1

558
 -1,858,842.6
 20,646
 337,290
 16.3
 3,758,977.2
 3,761,669.7
 81.2
 1.1
 17.7

930
 -1,847,528.8
 34,410
 337,290
 9.8
 3,763,877.6
 3,771,696.4
 81.6
 6.5
 11.9

1,395
 -1,834,624.0
 51,615
 337,290
 6.5
 3,772,478.0
 3,791,129.7
 87.1
 10.9
 2.0

2,789
 -1,799,245.4
 103,193
 337,290
 3.3
 3,804,876.8
 3,895,855.7
 93.4
 6.6
 0.0

Maximum likelihood (ML) analyses with nucleotide, codon, and amino acid substitution models and comparison of bootstrap probabilities (BPs) among trees 1 to 3. Concatenate (#c = 1) and separate analyses were performed for each dataset. The #c, #p, and #s represent the number of categories separated according to the total branch length of the 2,789 genes, the number of parameters, and the number of characters (or sites), respectively. AIC is the Akaike Information Criterion, and AICc is the AIC with second order correction. AIC with #s/#p > 40 and AICc with #s/#p < 40 are shown in italics. The best models based on AIC or AICc are shown in bold.

Nishihara et al. Genome Biology 2007 8:R199   doi:10.1186/gb-2007-8-9-r199

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