CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio
Codon frequencies: F3x4
Site-class models: PositiveSelection
ns = 3 ls = 6
Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0
TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0
Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0
TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0
--------------------------------------------------------------------------
Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0
CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0
CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0
CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0
--------------------------------------------------------------------------
Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0
ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0
ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0
Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0
--------------------------------------------------------------------------
Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0
GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0
GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0
GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0
--------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: test0
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000
position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333
#2: test1
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000
position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333
#3: test2
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000
position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0
TTC 0 | TCC 1 | TAC 0 | TGC 0
Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0
TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0
CTC 0 | CCC 1 | CAC 0 | CGC 0
CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0
CTG 0 | CCG 0 | CAG 0 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0
ATC 0 | ACC 0 | AAC 0 | AGC 0
ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0
Met M ATG 4 | ACG 2 | AAG 0 | AGG 0
------------------------------------------------------------------------------
Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0
GTC 0 | GCC 0 | GAC 0 | GGC 0
GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0
GTG 0 | GCG 0 | GAG 0 | GGG 0
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000
position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333
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.)
test0
test1 -1.0000 (0.0706 0.0000)
test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745)
TREE # 1: (1, 2, 3); MP score: 3
check convergence..
lnL(ntime: 3 np: 8): -30.819156 +0.000000
4..1 4..2 4..3
0.25573 0.00000 0.62424 5.28487 1.00000 0.00000 0.09213 1.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.87997
(1: 0.255727, 2: 0.000004, 3: 0.624239);
(test0: 0.255727, test1: 0.000004, test2: 0.624239);
Detailed output identifying parameters
kappa (ts/tv) = 5.28487
dN/dS for site classes (K=3)
p: 1.00000 0.00000 0.00000
w: 0.09213 1.00000 1.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2
4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0
4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0
Naive Empirical Bayes (NEB) analysis
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
Pr(w>1) post mean +- SE for w
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: 0.402 0.260 0.147 0.081 0.045 0.026 0.016 0.010 0.007 0.005
w2: 0.138 0.114 0.104 0.098 0.095 0.093 0.091 0.090 0.089 0.088
Posterior for p0-p1 (see the ternary graph)
0.001
0.001 0.002 0.003
0.001 0.001 0.002 0.003 0.006
0.000 0.001 0.001 0.002 0.004 0.006 0.010
0.000 0.000 0.001 0.001 0.003 0.004 0.007 0.011 0.016
0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.008 0.012 0.017 0.025
0.000 0.000 0.000 0.001 0.001 0.002 0.004 0.006 0.009 0.013 0.019 0.026 0.036
0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.004 0.006 0.009 0.014 0.019 0.027 0.037 0.049
0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.014 0.020 0.028 0.037 0.049 0.063
0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.015 0.020 0.027 0.036 0.046 0.061 0.075
sum of density on p0-p1 = 1.000000