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seed used = 861676029
4 258
Gorilla_gorilla ATG GCC AGG TAC AGA TGC TGT CGC AGC CAG AGC CGC AGC AGA TGT TAC CGG CAG AGC CGG AGC AGG TGT TAC CGG CAG AGA CAA AGC CAG AGC CGG AGC AGA TGC TAC CGG CAG AGC CAA AGC CGG AGC AGG TGT TAC CGG CAG AGA CAA AGA AGT CGC AGA CGT AGG CGG AGG AGC TGC CAG ACA CGG AGG AGA GCC ATG AGG TGC TGC CGC CGC AGG TAC AGA CTG AGA CGT AGA AGA CCC TAT CAT ATT GTA TCT
Hylobates_lar ATG GCC AGG TAC AGA TGC TGC CGC AGC CAG AGC CGG AGC AGA TGT TAC CGC CAG AGC CGG AGC AGA TGT TAC CGC CAG AGG CAA AGC CAG AGT CGG AGC AGA TGT TAC CGC CAG AGC CAG AGC CGG AGC AGA TGT TAC CGC CAG AGA CAA AGA AGT CGG AGA CGA AGG AGG CGG AGC TGC CAG ACA CGG AGG AGA GCC ATG AGG TGT --- CGC CGC AGG TAC AGG CTG AGA CGT AGA AGC TGT TAC CAC ATT GTA TCT
Pan_troglodytes ATG GCC AGG TAC AGA TGC TGT CGC AGC CAG AGC CGG AGC AGA TGT TAC CGG CAG AGA CGG AGC AGG TGT TAC CGG CAA AGG CAA AGC CAA AGT CGG AGC AGA TGT TAC CGG CAG AGC CAG AGA CGG AGC AGG TGT TAC CGG CAA AGA CAA AGA AGT CGC AGA CGA AGG CGA CGG AGC TGC CAG ACA CGG AGG AGA GCC ATG AGG TGC TGC CGC CGC AGG TAC AGA CTG AGA CGT AAA AGA TGT TAC CAT ATT GTA TCT
Papio_cynocephalus ATG GCC AGG TAC AGA TGC TGC CGC AGC CAG AGC CGA AGC AGA TGC TAT CGC CAG AGC CGG AGC AGA TGT AAC CGC CAG AGA CAG AGC CAA AGC CGG AGA AGC TGC TAT CGC CAG AGC CAA AGC CGG AGC AGA TGT TAC CGC CAG AGA CAG AGA AGT CGT AGA CGA AGG AGG CGA CGC TGC CAG ACA CGG AGG AGA GCC ATG AGG TGC TTC CGC CGC AGG TAC AGG CTG AGG CGT AGG AGG CCC TAT CAC ATC GTG TCT
Printing out site pattern counts
4 147 P
Gorilla_gorilla ACA AGA AGA AGA AGA AGA AGA AGA AGC AGC AGC AGC AGC AGG AGG AGG AGT ATG ATT CAA CAA CAG CAG CAG CAT CCC CGC CGC CGC CGG CGG CGG CGT CGT CTG GCC GTA TAC TAC TAC TAT TCT TGC TGC TGC TGC TGT TGT TGT
Hylobates_lar ACA AGA AGA AGA AGA AGC AGG AGG AGC AGC AGC AGC AGT AGA AGG CGG AGT ATG ATT CAA CAG CAG CAG CAG CAC TGT CGC CGG CGG AGG CGC CGG CGA CGT CTG GCC GTA TAC TAC TAC TAC TCT --- TGC TGT TGT TGC TGT TGT
Pan_troglodytes ACA AAA AGA AGA AGA AGA AGA AGG AGA AGC AGC AGC AGT AGG AGG CGG AGT ATG ATT CAA CAG CAA CAA CAG CAT TGT CGC CGC CGG CGA CGG CGG CGA CGT CTG GCC GTA TAC TAC TAC TAC TCT TGC TGC TGC TGT TGT TGT TGT
Papio_cynocephalus ACA AGG AGA AGC AGG AGG AGG AGA AGC AGA AGC CGC AGC AGA AGG CGA AGT ATG ATC CAG CAA CAA CAG CAG CAC CCC CGC CGT CGA AGG CGC CGG CGA CGT CTG GCC GTG AAC TAC TAT TAT TCT TTC TGC TGC TGC TGC TGC TGT
1 1 6 1 1 1 1 1 2 1 7 1 1 2 5
1 1 2 1 2 1 1 2 4 1 1 3 1 1 1
4 4 1 1 1 2 1 1 3 2 1 1 1 2 1
1 1 1 2
CODONML (in paml version 4.4, January 2010) algn
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
Site-class models: PositiveSelection
ns = 4 ls = 86
Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 | Ser TCT 1 1 1 1 | Tyr TAT 1 0 0 3 | Cys TGT 4 6 6 2
TTC 0 0 0 1 | TCC 0 0 0 0 | TAC 6 7 7 3 | TGC 5 3 4 6
Leu TTA 0 0 0 0 | TCA 0 0 0 0 | *** TAA 0 0 0 0 | *** TGA 0 0 0 0
TTG 0 0 0 0 | TCG 0 0 0 0 | TAG 0 0 0 0 | Trp TGG 0 0 0 0
--------------------------------------------------------------------------------------
Leu CTT 0 0 0 0 | Pro CCT 0 0 0 0 | His CAT 1 0 1 0 | Arg CGT 2 1 1 2
CTC 0 0 0 0 | CCC 1 0 0 1 | CAC 0 1 0 1 | CGC 5 7 4 8
CTA 0 0 0 0 | CCA 0 0 0 0 | Gln CAA 3 2 5 2 | CGA 0 1 2 3
CTG 1 1 1 1 | CCG 0 0 0 0 | CAG 7 8 5 8 | CGG 9 7 10 4
--------------------------------------------------------------------------------------
Ile ATT 1 1 1 0 | Thr ACT 0 0 0 0 | Asn AAT 0 0 0 0 | Ser AGT 1 2 2 1
ATC 0 0 0 1 | ACC 0 0 0 0 | AAC 0 0 0 1 | AGC 12 12 9 11
ATA 0 0 0 0 | ACA 1 1 1 1 | Lys AAA 0 0 1 0 | Arg AGA 12 11 12 10
Met ATG 2 2 2 2 | ACG 0 0 0 0 | AAG 0 0 0 0 | AGG 8 8 8 10
--------------------------------------------------------------------------------------
Val GTT 0 0 0 0 | Ala GCT 0 0 0 0 | Asp GAT 0 0 0 0 | Gly GGT 0 0 0 0
GTC 0 0 0 0 | GCC 2 2 2 2 | GAC 0 0 0 0 | GGC 0 0 0 0
GTA 1 1 1 0 | GCA 0 0 0 0 | Glu GAA 0 0 0 0 | GGA 0 0 0 0
GTG 0 0 0 1 | GCG 0 0 0 0 | GAG 0 0 0 0 | GGG 0 0 0 0
--------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: Gorilla_gorilla
position 1: T:0.19767 C:0.33721 A:0.43023 G:0.03488
position 2: T:0.05814 C:0.05814 A:0.20930 G:0.67442
position 3: T:0.12791 C:0.36047 A:0.19767 G:0.31395
Average T:0.12791 C:0.25194 A:0.27907 G:0.34109
#2: Hylobates_lar
position 1: T:0.20000 C:0.32941 A:0.43529 G:0.03529
position 2: T:0.05882 C:0.04706 A:0.21176 G:0.68235
position 3: T:0.12941 C:0.37647 A:0.18824 G:0.30588
Average T:0.12941 C:0.25098 A:0.27843 G:0.34118
#3: Pan_troglodytes
position 1: T:0.20930 C:0.33721 A:0.41860 G:0.03488
position 2: T:0.05814 C:0.04651 A:0.22093 G:0.67442
position 3: T:0.13953 C:0.30233 A:0.25581 G:0.30233
Average T:0.13566 C:0.22868 A:0.29845 G:0.33721
#4: Papio_cynocephalus
position 1: T:0.18605 C:0.34884 A:0.43023 G:0.03488
position 2: T:0.06977 C:0.05814 A:0.20930 G:0.66279
position 3: T:0.10465 C:0.40698 A:0.18605 G:0.30233
Average T:0.12016 C:0.27132 A:0.27519 G:0.33333
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 0 | Ser S TCT 4 | Tyr Y TAT 4 | Cys C TGT 18
TTC 1 | TCC 0 | TAC 23 | TGC 18
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 2 | Arg R CGT 6
CTC 0 | CCC 2 | CAC 2 | CGC 24
CTA 0 | CCA 0 | Gln Q CAA 12 | CGA 6
CTG 4 | CCG 0 | CAG 28 | CGG 30
------------------------------------------------------------------------------
Ile I ATT 3 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 6
ATC 1 | ACC 0 | AAC 1 | AGC 44
ATA 0 | ACA 4 | Lys K AAA 1 | Arg R AGA 45
Met M ATG 8 | ACG 0 | AAG 0 | AGG 34
------------------------------------------------------------------------------
Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0
GTC 0 | GCC 8 | GAC 0 | GGC 0
GTA 3 | GCA 0 | Glu E GAA 0 | GGA 0
GTG 1 | GCG 0 | GAG 0 | GGG 0
------------------------------------------------------------------------------
(Ambiguity data are not used in the counts.)
Codon position x base (3x4) table, overall
position 1: T:0.19825 C:0.33819 A:0.42857 G:0.03499
position 2: T:0.06122 C:0.05248 A:0.21283 G:0.67347
position 3: T:0.12536 C:0.36152 A:0.20700 G:0.30612
Average T:0.12828 C:0.25073 A:0.28280 G:0.33819
Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.00160053 0.00461550 0.00264274 0.00390828
0.00137189 0.00395614 0.00226521 0.00334996
0.00556376 0.01604434 0.00000000 0.00000000
0.01760588 0.05077045 0.00000000 0.04299111
0.00273032 0.00787349 0.00450821 0.00666707
0.00234028 0.00674871 0.00386418 0.00571463
0.00949113 0.02736976 0.01567140 0.02317601
0.03003357 0.08660842 0.04959031 0.07333778
0.00345998 0.00997762 0.00571299 0.00844879
0.00296570 0.00855224 0.00489685 0.00724182
0.01202755 0.03468409 0.01985944 0.02936960
0.03805978 0.10975378 0.06284289 0.09293667
0.00028245 0.00081450 0.00046637 0.00068970
0.00024210 0.00069814 0.00039974 0.00059117
0.00098184 0.00283135 0.00162118 0.00239752
0.00310692 0.00895949 0.00513003 0.00758667
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
Gorilla_gorilla
Hylobates_lar 0.0292 (0.0152 0.5209)
Pan_troglodytes 0.0947 (0.0254 0.2681) 0.0576 (0.0204 0.3547)
Papio_cynocephalus 0.0359 (0.0253 0.7047) 0.0740 (0.0360 0.4864) 0.0510 (0.0516 1.0128)
TREE # 1: ((2, (1, 3)), 4); MP score: -1
This is a rooted tree. Please check!
lnL(ntime: 6 np: 11): -517.824749 +0.000000
5..6 6..2 6..7 7..1 7..3 5..4
0.816965 0.181213 0.680999 0.410712 0.428524 0.753283 3.120348 0.987937 0.000000 0.098875 178.861466
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 3.27170
((2: 0.181213, (1: 0.410712, 3: 0.428524): 0.680999): 0.816965, 4: 0.753283);
((Hylobates_lar: 0.181213, (Gorilla_gorilla: 0.410712, Pan_troglodytes: 0.428524): 0.680999): 0.816965, Papio_cynocephalus: 0.753283);
Detailed output identifying parameters
kappa (ts/tv) = 3.12035
dN/dS (w) for site classes (K=3)
p: 0.98794 0.00000 0.01206
w: 0.09887 1.00000178.86147
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
5..6 0.817 163.8 94.2 2.2553 0.3417 0.1515 56.0 14.3
6..2 0.181 163.8 94.2 2.2553 0.0758 0.0336 12.4 3.2
6..7 0.681 163.8 94.2 2.2553 0.2849 0.1263 46.7 11.9
7..1 0.411 163.8 94.2 2.2553 0.1718 0.0762 28.1 7.2
7..3 0.429 163.8 94.2 2.2553 0.1793 0.0795 29.4 7.5
5..4 0.753 163.8 94.2 2.2553 0.3151 0.1397 51.6 13.2
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Gorilla_gorilla)
Pr(w>1) post mean +- SE for w
81 P 1.000** 178.855
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: Gorilla_gorilla)
Pr(w>1) post mean +- SE for w
81 P 0.963* 6.614 +- 2.783
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: 0.754 0.243 0.002 0.000 0.000 0.000 0.000 0.000 0.000 0.000
w2: 0.045 0.063 0.081 0.096 0.106 0.114 0.119 0.123 0.125 0.128
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 0.012
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 0.012 0.160
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 0.008 0.106 0.700
sum of density on p0-p1 = 1.000000
Time used: 0:12
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