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seed used = 1024006301
CODONML (in paml version 4.4, January 2010) ../Alignments/alignment.phylip
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
Site-class models:
ns = 5 ls = 74
Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 0 | Ser TCT 1 1 1 1 1 | Tyr TAT 0 0 1 0 0 | Cys TGT 3 2 3 3 3
TTC 1 1 1 1 1 | TCC 1 1 1 1 1 | TAC 1 1 0 1 1 | TGC 0 1 0 0 0
Leu TTA 0 0 0 0 0 | TCA 1 1 1 1 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 1 1 1 1 1 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Leu CTT 0 0 0 0 0 | Pro CCT 0 0 0 0 0 | His CAT 0 0 0 0 0 | Arg CGT 0 0 0 0 0
CTC 2 2 2 2 2 | CCC 1 1 1 1 1 | CAC 0 0 0 0 0 | CGC 0 0 0 0 0
CTA 1 1 1 1 1 | CCA 3 3 3 3 3 | Gln CAA 0 0 0 0 0 | CGA 1 1 1 1 1
CTG 3 3 3 3 3 | CCG 0 0 0 0 0 | CAG 1 1 1 1 1 | CGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Ile ATT 2 2 2 2 2 | Thr ACT 0 0 0 0 0 | Asn AAT 2 2 2 2 2 | Ser AGT 0 0 0 0 0
ATC 2 2 2 2 2 | ACC 0 0 0 0 0 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0
ATA 0 0 0 0 0 | ACA 2 2 2 2 2 | Lys AAA 5 5 5 5 5 | Arg AGA 2 2 2 2 2
Met ATG 3 3 3 3 3 | ACG 0 0 0 0 0 | AAG 5 5 5 5 5 | AGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Val GTT 3 3 3 3 1 | Ala GCT 0 0 0 0 0 | Asp GAT 2 2 2 2 2 | Gly GGT 0 0 0 0 0
GTC 0 0 0 0 1 | GCC 0 0 0 0 0 | GAC 4 4 4 4 4 | GGC 3 3 3 3 3
GTA 3 3 3 3 4 | GCA 0 0 0 0 0 | Glu GAA 8 8 8 8 8 | GGA 1 1 1 1 1
GTG 2 2 2 2 2 | GCG 0 0 0 0 0 | GAG 4 4 4 4 4 | GGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: Homo_sapie
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676
Average T:0.20270 C:0.16216 A:0.36937 G:0.26577
#2: Pan_troglo
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.16216 C:0.21622 A:0.36486 G:0.25676
Average T:0.19820 C:0.16667 A:0.36937 G:0.26577
#3: Gorilla_go
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.18919 C:0.18919 A:0.36486 G:0.25676
Average T:0.20721 C:0.15766 A:0.36937 G:0.26577
#4: Pongo_pygm
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676
Average T:0.20270 C:0.16216 A:0.36937 G:0.26577
#5: Macaca_mul
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.14865 C:0.21622 A:0.37838 G:0.25676
Average T:0.19369 C:0.16667 A:0.37387 G:0.26577
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 0 | Ser S TCT 5 | Tyr Y TAT 1 | Cys C TGT 14
TTC 5 | TCC 5 | TAC 4 | TGC 1
Leu L TTA 0 | TCA 5 | *** * TAA 0 | *** * TGA 0
TTG 5 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 0 | Pro P CCT 0 | His H CAT 0 | Arg R CGT 0
CTC 10 | CCC 5 | CAC 0 | CGC 0
CTA 5 | CCA 15 | Gln Q CAA 0 | CGA 5
CTG 15 | CCG 0 | CAG 5 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 10 | Thr T ACT 0 | Asn N AAT 10 | Ser S AGT 0
ATC 10 | ACC 0 | AAC 0 | AGC 0
ATA 0 | ACA 10 | Lys K AAA 25 | Arg R AGA 10
Met M ATG 15 | ACG 0 | AAG 25 | AGG 0
------------------------------------------------------------------------------
Val V GTT 13 | Ala A GCT 0 | Asp D GAT 10 | Gly G GGT 0
GTC 1 | GCC 0 | GAC 20 | GGC 15
GTA 16 | GCA 0 | Glu E GAA 40 | GGA 5
GTG 10 | GCG 0 | GAG 20 | GGG 0
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17027 C:0.20541 A:0.36757 G:0.25676
Average T:0.20090 C:0.16306 A:0.37027 G:0.26577
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
Homo_sapie
Pan_troglo 0.0000 (0.0000 0.0207)
Gorilla_go 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0421)
Pongo_pygm -1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0207)
Macaca_mul 0.0000 (0.0000 0.0421) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0421)
Model 0: one-ratio
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 9): -308.032819 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013437 0.013431 0.000004 0.027837 1.519174 0.000100
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013437): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027837);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013437): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027837);
Detailed output identifying parameters
kappa (ts/tv) = 1.51917
omega (dN/dS) = 0.00010
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0001 0.0000 0.0379 0.0 2.1
tree length for dN: 0.0000
tree length for dS: 0.0746
Time used: 0:01
Model 1: NearlyNeutral (2 categories)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
check convergence..
lnL(ntime: 7 np: 10): -308.031692 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518319 0.999990 0.000001
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839);
Detailed output identifying parameters
kappa (ts/tv) = 1.51832
dN/dS (w) for site classes (K=2)
p: 0.99999 0.00001
w: 0.00000 1.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1
Time used: 0:04
Model 2: PositiveSelection (3 categories)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
check convergence..
lnL(ntime: 7 np: 12): -308.031579 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518257 1.000000 0.000000 0.000001 1.000000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839);
Detailed output identifying parameters
kappa (ts/tv) = 1.51826
dN/dS (w) for site classes (K=3)
p: 1.00000 0.00000 0.00000
w: 0.00000 1.00000 1.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1
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%)
(amino acids refer to 1st sequence: Homo_sapie)
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: 0.668 0.219 0.073 0.025 0.009 0.003 0.001 0.001 0.000 0.000
w2: 0.281 0.168 0.120 0.093 0.076 0.065 0.057 0.051 0.046 0.043
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 0.001
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.020
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.004 0.014 0.058
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.004 0.011 0.040 0.168
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 0.002 0.005 0.012 0.033 0.118 0.484
sum of density on p0-p1 = 1.000000
Time used: 0:15
Model 3: discrete (3 categories)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 13): -308.031579 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518243 0.195153 0.461061 0.000001 0.000001 0.000001
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839);
Detailed output identifying parameters
kappa (ts/tv) = 1.51824
dN/dS (w) for site classes (K=3)
p: 0.19515 0.46106 0.34379
w: 0.00000 0.00000 0.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1
Naive Empirical Bayes (NEB) analysis
Time used: 0:18
Model 7: beta (10 categories)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
check convergence..
lnL(ntime: 7 np: 10): -308.031567 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518240 0.005000 99.000000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839);
Detailed output identifying parameters
kappa (ts/tv) = 1.51824
Parameters in M7 (beta):
p= 0.00500 q= 99.00000
dN/dS (w) for site classes (K=10)
p: 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000
w: 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1
Time used: 0:56
Model 8: beta&w>1 (11 categories)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 12): -308.031680 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518304 0.999990 0.005000 99.000000 1.000000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839);
Detailed output identifying parameters
kappa (ts/tv) = 1.51830
Parameters in M8 (beta&w>1):
p0= 0.99999 p= 0.00500 q= 99.00000
(p1= 0.00001) w= 1.00000
dN/dS (w) for site classes (K=11)
p: 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.10000 0.00001
w: 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
6..7 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0000 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0000 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0000 0.0000 0.0379 0.0 2.1
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%)
(amino acids refer to 1st sequence: Homo_sapie)
Pr(w>1) post mean +- SE for w
The grid
p0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
p : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900
q : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900
ws: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500
Posterior on the grid
p0: 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.014 0.082 0.899
p : 0.628 0.200 0.082 0.039 0.021 0.012 0.007 0.005 0.003 0.002
q : 0.001 0.015 0.037 0.061 0.086 0.111 0.136 0.160 0.184 0.209
ws: 0.332 0.183 0.122 0.088 0.068 0.055 0.046 0.040 0.035 0.031
Time used: 1:49
|
