| blob | bd15f69dd2b62ff8feb99f7e40781e419b87c31c |
2 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG
3 Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA
4 Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA
5 Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG
6 Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG
7 Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA
8 Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA
11 CODONML (in paml 3.13, August 2002) lysozymeSmall.txt Model: One dN/dS ratio dGamma (ncatG=11)
12 Codon frequencies: F3x4
13 Warning: Gamma model for codons. See documentation.Site-class models
15 ns = 7 ls = 130
16 # site patterns = 81
17 2 1 1 1 2 7 2 3 3 1 2 2 2 1 1
18 5 1 4 3 2 1 1 3 1 5 4 5 1 1 1
19 1 2 1 3 2 1 1 1 1 1 1 1 2 2 1
20 1 1 1 1 1 2 2 1 1 1 1 1 1 3 1
21 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
22 1 1 1 1 1 1
24 1
25 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG ATC AGC CTA GCA AAC TGG ATG AGT GGT TAC ACA CGA GCT AAT GCT GAC AGA TAT GGG ATA TTT CAG ATC CGC TAC AAT GAT AAA ACC CCA GTT AAT CAT TTA TCC TGC AGT CAA GAT AAC GCT GAT GTA GCT GTC CGT ATT AGA GTG AGA AAT CGT AGA GTC CGT TAT GTT CAA GGT GTG
26 Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A
27 Cgu/Can_colobus ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GAC ... ... C.. ..T GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... A.. ... ... ... ... ... ... A.. ... C.. ... .A. ..G .AC ... ... A.. ... ... G.. ... ..A
28 Pne_langur ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GA. ... ... C.. ... GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... G.. ... A.. ... ... ... ... A.C ... ... ... ... ... ... A.. G.. C.. ... ... ... .AC .A. ... A.. ..C ... A.. ... ...
29 Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ...
30 Ssc_squirrelM ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G C.T ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ... A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. C.A ..G ..C ... ... ... ... ... .A. GC. .A. ... ... A.. ... ... ... ... ..A
31 Cja_marmoset ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..T ... C.. ... ... ... ... ... ... ... ... ... ... ... ... .A. ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ..C A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. ..A ..G ..C ... ..C ... ..G ... .A. GC. .A. ... ... A.. ... ... ... ... ..A
33 Codon usage in sequences
34 --------------------------------------------------------------------------------------------------------------
35 Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7
36 TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1
37 Leu TTA 1 1 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
38 TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5
39 --------------------------------------------------------------------------------------------------------------
40 Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2
41 CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0
42 CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0
43 CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0
44 --------------------------------------------------------------------------------------------------------------
45 Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2
46 ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3
47 ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4
48 Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4
49 --------------------------------------------------------------------------------------------------------------
50 Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1
51 GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3
52 GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5
53 GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1
54 --------------------------------------------------------------------------------------------------------------
56 --------------------------------------------------
57 Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7
58 TTC 0 | TCC 1 | TAC 2 | TGC 1
59 Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0
60 TTG 3 | TCG 0 | TAG 0 | Trp TGG 5
61 --------------------------------------------------
62 Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1
63 CTC 0 | CCC 0 | CAC 1 | CGC 1
64 CTA 1 | CCA 2 | Gln CAA 5 | CGA 0
65 CTG 3 | CCG 0 | CAG 2 | CGG 0
66 --------------------------------------------------
67 Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2
68 ATC 3 | ACC 1 | AAC 5 | AGC 3
69 ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3
70 Met ATG 1 | ACG 0 | AAG 2 | AGG 5
71 --------------------------------------------------
72 Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1
73 GTC 3 | GCC 4 | GAC 2 | GGC 3
74 GTA 1 | GCA 5 | Glu GAA 2 | GGA 5
75 GTG 2 | GCG 0 | GAG 2 | GGG 1
76 --------------------------------------------------
78 Codon position x base (3x4) table for each sequence.
80 #1: Hsa_Human
81 position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615
82 position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077
83 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
85 #2: Hla_gibbon
86 position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308
87 position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308
88 position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462
90 #3: Cgu/Can_colobus
91 position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385
92 position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692
93 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
95 #4: Pne_langur
96 position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154
97 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462
98 position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231
100 #5: Mmu_rhesus
101 position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538
102 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462
103 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
105 #6: Ssc_squirrelM
106 position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077
107 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231
108 position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231
110 #7: Cja_marmoset
111 position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846
112 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231
113 position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000
115 Sums of codon usage counts
116 ------------------------------------------------------------------------------
117 Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49
118 TTC 1 | TCC 7 | TAC 21 | TGC 7
119 Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0
120 TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35
121 ------------------------------------------------------------------------------
122 Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8
123 CTC 1 | CCC 0 | CAC 6 | CGC 6
124 CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4
125 CTG 18 | CCG 0 | CAG 14 | CGG 0
126 ------------------------------------------------------------------------------
127 Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17
128 ATC 22 | ACC 7 | AAC 35 | AGC 21
129 ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28
130 Met M ATG 7 | ACG 0 | AAG 17 | AGG 22
131 ------------------------------------------------------------------------------
132 Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11
133 GTC 19 | GCC 24 | GAC 10 | GGC 21
134 GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35
135 GTG 15 | GCG 0 | GAG 14 | GGG 7
136 ------------------------------------------------------------------------------
139 Codon position x base (3x4) table, overall
141 position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846
142 position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780
143 position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231
145 Codon frequencies under model, for use in evolver:
146 0.01378574 0.00962226 0.01059374 0.00809565
147 0.01181635 0.00824765 0.00908035 0.00693913
148 0.02279949 0.01591374 0.00000000 0.00000000
149 0.02052711 0.01432765 0.00000000 0.01205451
150 0.00941649 0.00657258 0.00723616 0.00552982
151 0.00807127 0.00563364 0.00620242 0.00473984
152 0.01557342 0.01087004 0.01196749 0.00914546
153 0.01402125 0.00978665 0.01077472 0.00823396
154 0.02214758 0.01545871 0.01701945 0.01300613
155 0.01898364 0.01325032 0.01458810 0.01114811
156 0.03662868 0.02556633 0.02814755 0.02151013
157 0.03297798 0.02301819 0.02534214 0.01936627
158 0.02320222 0.01619484 0.01782990 0.01362547
159 0.01988762 0.01388129 0.01528277 0.01167897
160 0.03837291 0.02678377 0.02948791 0.02253443
161 0.03454836 0.02411429 0.02654891 0.02028847
165 Nei & Gojobori 1986. dN/dS (dN, dS)
166 (Note: This matrix is not used in later m.l. analysis.
167 Use runmode = -2 for ML pairwise comparison.)
169 Hsa_Human
170 Hla_gibbon 0.2782 (0.0133 0.0478)
171 Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671)
172 Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484)
173 Mmu_rhesus 1.8744 (0.0562 0.0300) 1.0215 (0.0561 0.0550) 1.2973 (0.0473 0.0364) 1.3970 (0.0508 0.0364)
174 Ssc_squirrelM 0.4701 (0.0633 0.1346) 0.4688 (0.0633 0.1349) 0.5159 (0.0775 0.1502) 0.5833 (0.0959 0.1645) 0.4544 (0.0559 0.1230)
175 Cja_marmoset 0.4725 (0.0634 0.1341) 0.5925 (0.0633 0.1069) 0.4702 (0.0704 0.1496) 0.5411 (0.0886 0.1638) 0.3995 (0.0490 0.1225) 0.1595 (0.0099 0.0619)
178 Model 0: one-ratio
180 TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
181 check convergence..
182 lnL(ntime: 11 np: 14): -906.017440 +0.000000
183 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
184 0.06798 0.02556 0.03889 0.04345 0.07637 0.04379 0.05254 0.02168 0.12266 0.04080 0.02392 4.54006 0.80663 0.50000
185 SEs for parameters:
186 0.02557 0.01516 0.01844 0.02016 0.02668 0.01990 0.02155 0.01551 0.03392 0.01916 0.01506 0.23600 0.23600 -1.00000
187 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
189 tree length = 0.55765
191 ((1: 0.02556, 2: 0.03889): 0.06798, ((3: 0.04379, 4: 0.05254): 0.07637, 5: 0.02168): 0.04345, (6: 0.04080, 7: 0.02392): 0.12266);
193 ((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, ((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254): 0.07637, Mmu_rhesus: 0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): 0.12266);
195 Detailed output identifying parameters
196 kappa (ts/tv) = 4.54006
198 alpha (gamma) = 0.50000
199 r ( 1): 1.00000
200 f: 1.00000
202 dN & dS for each branch
204 branch t S N dN/dS dN dS S*dS N*dN
206 8..9 0.068 107.8 282.2 0.8066 0.0213 0.0263 2.8 6.0
207 9..1 0.026 107.8 282.2 0.8066 0.0080 0.0099 1.1 2.3
208 9..2 0.039 107.8 282.2 0.8066 0.0122 0.0151 1.6 3.4
209 8..10 0.043 107.8 282.2 0.8066 0.0136 0.0168 1.8 3.8
210 10..11 0.076 107.8 282.2 0.8066 0.0239 0.0296 3.2 6.7
211 11..3 0.044 107.8 282.2 0.8066 0.0137 0.0170 1.8 3.9
212 11..4 0.053 107.8 282.2 0.8066 0.0164 0.0204 2.2 4.6
213 10..5 0.022 107.8 282.2 0.8066 0.0068 0.0084 0.9 1.9
214 8..12 0.123 107.8 282.2 0.8066 0.0383 0.0475 5.1 10.8
215 12..6 0.041 107.8 282.2 0.8066 0.0128 0.0158 1.7 3.6
216 12..7 0.024 107.8 282.2 0.8066 0.0075 0.0093 1.0 2.1
219 Time used: 00:02:05
222 Model 1: neutral (2 categories)
224 TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
225 lnL(ntime: 11 np: 14): -902.503869 +0.000000
226 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
227 0.06961 0.02556 0.03938 0.04422 0.07778 0.04414 0.05228 0.02134 0.12574 0.04157 0.02367 4.29790 0.41271 0.50000
228 SEs for parameters:
229 0.02665 0.01541 0.01888 0.02101 0.02769 0.02034 0.02188 0.01585 0.03565 0.01971 0.01530 -1.00000 -1.00000 -1.00000
230 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
232 tree length = 0.56528
234 ((1: 0.02556, 2: 0.03938): 0.06961, ((3: 0.04414, 4: 0.05228): 0.07778, 5: 0.02134): 0.04422, (6: 0.04157, 7: 0.02367): 0.12574);
236 ((Hsa_Human: 0.02556, Hla_gibbon: 0.03938): 0.06961, ((Cgu/Can_colobus: 0.04414, Pne_langur: 0.05228): 0.07778, Mmu_rhesus: 0.02134): 0.04422, (Ssc_squirrelM: 0.04157, Cja_marmoset: 0.02367): 0.12574);
238 Detailed output identifying parameters
239 kappa (ts/tv) = 4.29790
242 dN/dS for site classes (K=2)
243 p: 0.41271 0.58729
244 w: 0.00000 1.00000
246 alpha (gamma) = 0.41271
247 r ( 2): 0.00000 1.00000
248 f: 0.41271 0.58729
250 dN & dS for each branch
252 branch t S N dN/dS dN dS S*dS N*dN
254 8..9 0.070 107.1 282.9 0.5873 0.0195 0.0331 3.5 5.5
255 9..1 0.026 107.1 282.9 0.5873 0.0071 0.0122 1.3 2.0
256 9..2 0.039 107.1 282.9 0.5873 0.0110 0.0187 2.0 3.1
257 8..10 0.044 107.1 282.9 0.5873 0.0124 0.0210 2.3 3.5
258 10..11 0.078 107.1 282.9 0.5873 0.0217 0.0370 4.0 6.1
259 11..3 0.044 107.1 282.9 0.5873 0.0123 0.0210 2.2 3.5
260 11..4 0.052 107.1 282.9 0.5873 0.0146 0.0249 2.7 4.1
261 10..5 0.021 107.1 282.9 0.5873 0.0060 0.0102 1.1 1.7
262 8..12 0.126 107.1 282.9 0.5873 0.0351 0.0598 6.4 9.9
263 12..6 0.042 107.1 282.9 0.5873 0.0116 0.0198 2.1 3.3
264 12..7 0.024 107.1 282.9 0.5873 0.0066 0.0113 1.2 1.9
267 Time used: 00:05:26
270 Model 2: selection (3 categories)
272 TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
273 check convergence..
274 lnL(ntime: 11 np: 16): -900.076500 +0.000000
275 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
276 0.07903 0.02598 0.04137 0.04535 0.08550 0.04486 0.05417 0.01935 0.13948 0.04319 0.02492 5.12250 0.38160 0.54916 6.17292 0.41271
277 SEs for parameters:
278 0.03226 0.01618 0.02021 0.02390 0.03229 0.02158 0.02363 0.01746 0.04358 0.02088 0.01602 1.50414 0.14016 0.16630 4.30113 -1.00000
279 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
281 tree length = 0.60321
283 ((1: 0.02598, 2: 0.04137): 0.07903, ((3: 0.04486, 4: 0.05417): 0.08550, 5: 0.01935): 0.04535, (6: 0.04319, 7: 0.02492): 0.13948);
285 ((Hsa_Human: 0.02598, Hla_gibbon: 0.04137): 0.07903, ((Cgu/Can_colobus: 0.04486, Pne_langur: 0.05417): 0.08550, Mmu_rhesus: 0.01935): 0.04535, (Ssc_squirrelM: 0.04319, Cja_marmoset: 0.02492): 0.13948);
287 Detailed output identifying parameters
288 kappa (ts/tv) = 5.12250
291 dN/dS for site classes (K=3)
292 p: 0.38160 0.54916 0.06924
293 w: 0.00000 1.00000 6.17292
295 alpha (gamma) = 0.38160
296 r ( 3): 0.00000 1.00000 6.17292
297 f: 0.38160 0.54916 0.06924
299 dN & dS for each branch
301 branch t S N dN/dS dN dS S*dS N*dN
303 8..9 0.079 109.3 280.7 0.9766 0.0262 0.0268 2.9 7.3
304 9..1 0.026 109.3 280.7 0.9766 0.0086 0.0088 1.0 2.4
305 9..2 0.041 109.3 280.7 0.9766 0.0137 0.0140 1.5 3.8
306 8..10 0.045 109.3 280.7 0.9766 0.0150 0.0154 1.7 4.2
307 10..11 0.086 109.3 280.7 0.9766 0.0283 0.0290 3.2 7.9
308 11..3 0.045 109.3 280.7 0.9766 0.0149 0.0152 1.7 4.2
309 11..4 0.054 109.3 280.7 0.9766 0.0179 0.0184 2.0 5.0
310 10..5 0.019 109.3 280.7 0.9766 0.0064 0.0066 0.7 1.8
311 8..12 0.139 109.3 280.7 0.9766 0.0462 0.0473 5.2 13.0
312 12..6 0.043 109.3 280.7 0.9766 0.0143 0.0146 1.6 4.0
313 12..7 0.025 109.3 280.7 0.9766 0.0083 0.0085 0.9 2.3
317 Positively selected sites Prob(w>1):
319 15 L 0.6588
320 17 M 0.6601
321 37 G 0.7155
322 41 R 0.9282
323 50 R 0.8292
324 62 R 0.5229
325 114 N 0.6491
326 126 Q 0.5226
329 Time used: 00:13:43