seed used = 739250845
CODONML (in paml version 4.3, August 2009) abglobin.nuc
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
Site-class models:
ns = 5 ls = 285
Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2
TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3
Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4
--------------------------------------------------------------------------------------------------
Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1
CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0
CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0
CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0
--------------------------------------------------------------------------------------------------
Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1
ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3
ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2
Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2
--------------------------------------------------------------------------------------------------
Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10
GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5
GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3
GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2
--------------------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: human
position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649
position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333
position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140
Average T:0.20468 C:0.31345 A:0.18480 G:0.29708
#2: goat-cow
position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000
position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035
position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088
Average T:0.21988 C:0.29123 A:0.19181 G:0.29708
#3: rabbit
position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140
position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684
position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439
Average T:0.21053 C:0.29708 A:0.20819 G:0.28421
#4: rat
position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895
position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439
position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421
Average T:0.22924 C:0.28421 A:0.21404 G:0.27251
#5: marsupial
position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439
position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333
position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123
Average T:0.24211 C:0.29240 A:0.20585 G:0.25965
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8
TTC 51 | TCC 31 | TAC 19 | TGC 9
Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0
TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16
------------------------------------------------------------------------------
Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7
CTC 24 | CCC 25 | CAC 68 | CGC 1
CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0
CTG 123 | CCG 5 | CAG 25 | CGG 2
------------------------------------------------------------------------------
Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13
ATC 12 | ACC 53 | AAC 35 | AGC 19
ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3
Met M ATG 17 | ACG 0 | AAG 98 | AGG 17
------------------------------------------------------------------------------
Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30
GTC 19 | GCC 92 | GAC 48 | GGC 60
GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7
GTG 89 | GCG 14 | GAG 40 | GGG 7
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825
position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965
position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842
Average T:0.22129 C:0.29567 A:0.20094 G:0.28211
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)
human
goat-cow 0.2507 (0.0863 0.3443)
rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581)
rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187)
marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852)
Model 1: NearlyNeutral (2 categories)
TREE # 1: (((3, 4), 1), 2, 5); MP score: 387
lnL(ntime: 7 np: 10): -2970.527521 +0.000000
6..7 7..8 8..3 8..4 7..1 6..2 6..5
0.081884 0.073268 0.252707 0.649536 0.215600 0.223230 1.401893 2.066843 0.826211 0.065970
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 2.89812
(((3: 0.252707, 4: 0.649536): 0.073268, 1: 0.215600): 0.081884, 2: 0.223230, 5: 1.401893);
(((rabbit: 0.252707, rat: 0.649536): 0.073268, human: 0.215600): 0.081884, goat-cow: 0.223230, marsupial: 1.401893);
Detailed output identifying parameters
kappa (ts/tv) = 2.06684
dN/dS (w) for site classes (K=2)
p: 0.82621 0.17379
w: 0.06597 1.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.082 663.8 191.2 0.2283 0.0155 0.0681 10.3 13.0
7..8 0.073 663.8 191.2 0.2283 0.0139 0.0609 9.2 11.7
8..3 0.253 663.8 191.2 0.2283 0.0480 0.2101 31.8 40.2
8..4 0.650 663.8 191.2 0.2283 0.1233 0.5401 81.8 103.3
7..1 0.216 663.8 191.2 0.2283 0.0409 0.1793 27.2 34.3
6..2 0.223 663.8 191.2 0.2283 0.0424 0.1856 28.1 35.5
6..5 1.402 663.8 191.2 0.2283 0.2661 1.1656 176.6 222.9
Naive Empirical Bayes (NEB) analysis
Time used: 0:08
Model 2: PositiveSelection (3 categories)
TREE # 1: (((3, 4), 1), 2, 5); MP score: 387
lnL(ntime: 7 np: 12): -2965.809712 +0.000000
6..7 7..8 8..3 8..4 7..1 6..2 6..5
0.100782 0.089538 0.293059 0.801779 0.242098 0.264641 1.797878 2.181363 0.833468 0.136461 0.072723 6.285989
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 3.58978
(((3: 0.293059, 4: 0.801779): 0.089538, 1: 0.242098): 0.100782, 2: 0.264641, 5: 1.797878);
(((rabbit: 0.293059, rat: 0.801779): 0.089538, human: 0.242098): 0.100782, goat-cow: 0.264641, marsupial: 1.797878);
Detailed output identifying parameters
kappa (ts/tv) = 2.18136
dN/dS (w) for site classes (K=3)
p: 0.83347 0.13646 0.03007
w: 0.07272 1.00000 6.28599
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.101 662.3 192.7 0.3861 0.0247 0.0641 16.4 12.3
7..8 0.090 662.3 192.7 0.3861 0.0220 0.0569 14.6 11.0
8..3 0.293 662.3 192.7 0.3861 0.0719 0.1863 47.6 35.9
8..4 0.802 662.3 192.7 0.3861 0.1968 0.5096 130.3 98.2
7..1 0.242 662.3 192.7 0.3861 0.0594 0.1539 39.4 29.6
6..2 0.265 662.3 192.7 0.3861 0.0649 0.1682 43.0 32.4
6..5 1.798 662.3 192.7 0.3861 0.4412 1.1428 292.2 220.2
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)
Pr(w>1) post mean +- SE for w
35 S 0.643 4.400
111 A 0.736 4.890
115 A 0.785 5.151
131 S 0.704 4.722
144 P 0.794 5.198
215 A 0.799 5.225
226 T 0.560 3.962
264 P 0.971* 6.134
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)
Pr(w>1) post mean +- SE for w
35 S 0.634 4.600 +- 3.257
111 A 0.727 5.133 +- 3.164
115 A 0.779 5.538 +- 3.111
131 S 0.706 5.170 +- 3.273
144 P 0.781 5.485 +- 3.082
195 G 0.502 3.842 +- 3.253
215 A 0.788 5.577 +- 3.082
226 T 0.572 4.307 +- 3.325
264 P 0.964* 6.573 +- 2.443
The grid (see ternary graph for p0-p1)
w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500
Posterior on the grid
w0: 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
w2: 0.006 0.033 0.085 0.129 0.147 0.146 0.135 0.121 0.106 0.092
Posterior for p0-p1 (see the ternary graph)
0.000
0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.199
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.100 0.700
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000
sum of density on p0-p1 = 1.000000
Time used: 0:26
Time used: 0:26